tpwis-2018sanjeeva/wp-content/uploads/... · bombay, india from 24th to 28th february, 2018....

Proteomics Boot camp www.bio.iitb.ac.in/~sanjeeva/massfiitb

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Welcome messageDear Colleagues,

We are pleased to announce the “Targeted Proteomics Workshop and International Symposium (TPWIS-2018)” to be held at the Indian Institute of Technology (IIT) Bombay, India from 24th to 28th February, 2018. Advancements in proteomics

have been phenomenal over the last decade with several promising high-throughput technologies emerging at the forefront of various applications. Owing to the rapid advancements in state-of-the-art proteomics technologies, continuous expansion of our scientific understanding, and challenges associated with omics research, it has become essential to keep up with current trends and advances in proteomics research. In this light, we are conducting a series of parallel workshops from 24th to 28th February 2018, at IIT Bombay where eminent scientists and researchers from India and abroad would be sharing their knowledge and expertise to train the participants and familiarize them to the vast applications of proteomics.

This event will cover topics like targeted methods and statistical tools required for designing a proteomic study. Primarily, the focus will be on Single Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM), Absolute Protein Quantification, popular platforms like Skyline, experimental design, quality control, data analysis, downstream processing of data and other subjects that are integral to targeted proteomics. This event will also include a Mass Spectrometry (MS) workshop aiming at the basic understanding of sample run, data acquisition and data analysis that will be conducted in the newly founded Mass spectrometry facility at IIT Bombay. Additionally, a course on Interactomics will be conducted at IIT Bombay as approved by the Global Initiative of Academic Networks (GIAN). This five-day long course will have stimulating lectures delivered by the course co-ordinators, hands-on experiments for microarrays, label-free biosensors and next generation sequencing platforms, in addition to various eminent talks by industry speakers. A one-day international symposium is also part of the whole event wherein various researchers and scientists will come forward together and educate the young audience with several approaches and applications of proteomics. Interestingly, we have also scheduled a Satellite symposium on Targeted Proteomics at IIT Goa, one of the budding and sprawling IITs’ of the country. Aimed at enlightening the young, enthusiastic engineering minds about the different realms of proteomics, the event has gained a lot of momentum.

We anticipate that Targeted Proteomics workshop and International Symposium will accelerate the establishment of global standards for data acquisition, analysis, comparison, exchange and verification, which is crucial in successful translational of proteomics research. This focused event will undoubtedly be a great opportunity for the students, young researchers and industry experts to get familiarized with recent advances and significant achievements in proteomics research.

Sincerely yours,Dr. Sanjeeva SrivastavaConvener, Targeted Proteomics Workshop & International Symposium TPWIS-2018Associate Professor Department of Biosciences & BioengineeringIIT Bombay, Mumbai, India


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INDEX

S. NO CONTENT PAGE NO.

1 WORKSHOP I - Targeted Proteomics 6

2 WORKSHOP II - MS Workshop 16

3 WORKSHOP III - Interactomics 27

4 INTERNATIONAL SYMPOSIUM IIT BOMBAY 42

5 CULTURAL EVENING 60

6 SATELLITE SYMPOSIUM IIT GOA 63

7 GENERAL INFORMTION

a. Proteomics milestones

b. About HUPO

c. About PSI

d. Outreach efforts: Proteomics Documentaries.

e. About IIT Bombay

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68

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8 SPONSOR / PARTNERS PROFILE 949 FLOOR PLAN 9910 AUTHOR INDEX / UPCOMING EVENT 100


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WORKSHOP : 1


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Workshop I:TARGETED PROTEOMICS


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Preamble to the Targeted Proteomics Workshop

Major advances have been achieved in various facets of targeted proteomics, including advances in instrumentation, the generation of SRM, PRM and SWATH/DIA assay libraries, and the development of multiple computational tools for every

step of a targeted proteomics workflow. While these advances have enabled the successful application of the targeted workflows by an increasing number of laboratories worldwide, it has become evident that applying SRM, PRM or SWATH/DIA requires interdisciplinary knowledge and experience in three interlaced aspects: designing biological questions which can be investigated by targeted proteomics, harnessing the current technologies to their full capacity and applying a set of computational tools and bioinformatics resources for every step of a targeted proteomics workflow. We believe that overcoming the barriers within and between these aspects would enable a wide and routine application of targeted proteomics in systems biology.

The Targeted Proteomics Workshop is scheduled from 24th – 27th Feb, 2018. Mr. Brendan MacLean from University of Washington, Dr. Cristina Chiva and Dr. Eva Borras from CRG/UPF Proteomics Unit at Barcelona, Spain and Dr. Nathalie Selevsek from Functional Genomics Center, Zurich would be conducting this workshop, wherein they will explain the importance and concepts of targeted proteomics and guide the participants via a step-by-step tutorial for data analysis using Skyline.Targeted Proteomics Workshop schedule

Targeted Proteomics Workshop schedule(24th to 27th feb, 2018)

DAY-1 (SATURDAY, 24TH FEBRUARY 2018)VENUE: SEMINAR ROOM NO. 11,V.M.C.C. Ist FLOOR

08:15 - 08:30 AM Opening remarks – by Mr. Brendan MacLean08:30 - 09:30 AM Lecture: Why targeted proteomics? – by Dr. Eva Bor-

ràs09:30 - 10:30 AM Lecture: Introduction to Skyline – by Mr. Brendan

MacLean10:30 - 11:00 AM Tea break11:00 - 12:00 PM Lecture: Introduction to SRM and PRM – by Dr. Eva

Borràs11:30 - 01:00 PM Hands-on: Targeted method editing – by Mr. Brendan

MacLean01:00 - 02:00 PM Lunch02:00 - 02:15 PM Lecture: Introduction to the tutorials – by Dr. Cristina

Chiva


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02:15 - 04:45 PM Tutorial 1: Setting up Parallel (and Selected) reaction monitoring methods – by Drs. Cristina Chiva & Nath-alie Selevsek

DAY-2 (SUNDAY, 25TH FEBRUARY 2018)08:30 - 09:30 AM Lecture: Quantitative targeted proteomics – by Dr.

Cristina Chiva09:30 - 10:30 AM Hands-on: Effective data processing and analysis with

Skyline – by Mr. Brendan MacLean10:30 - 11:00 AM Tea break11:00 - 12:00 PM Hands on: Statistical peak picking model – by Mr.

Brendan MacLean12:00 - 01:00 PM Tutorial 2: Parallel reaction monitoring data analysis –

by Drs. Cristina Chiva & Eva Borràs01:00 - 02:00 PM Lunch02:00 - 03:30 PM Ctd. Tutorial 2: Parallel reaction monitoring data anal-

ysis – by Drs. Cristina Chiva & Eva Borràs03:30 - 04:45 PM Hands-on: Group comparisons with Skyline – by Mr.

Brendan MacLean

DAY-3 (MONDAY, 26TH FEBRUARY 2018)08:30 - 09:30 AM Lecture: Analyzing post-translational modifications

with PRM – by Dr. Nathalie Selevsek09:30 - 10:30 AM Lecture: Advanced PRM methods – by Dr. Cristina

Chiva10:30 - 11:00 AM Tea break11:00 - 01:00 PM Hands-on: Retention time prediction with iRT in Sky-

line – by Mr. Brendan MacLean01:00 - 2:00 PM Lunch02:00 - 03:00 PM Lecture: Small molecule analysis with Skyline – by Mr.

Brendan MacLean03:00 - 04:45 PM Hands-on: External calibrations curves – by Mr. Bren-

dan McLean

DAY-4 TUESDAY, 27TH FEBRUARY 2018)08:30 - 09:30 AM Lecture: Introduction to data independent acquisition

– by Dr. Nathalie Selevsek09:30 - 10:30 AM Tutorial 3: DIA data analysis in Skyline – by Drs. Eva

Borràs & Nathalie Selevsek10:30 - 11:00 AM Tea break11:00 - 01:00 PM Continuation Tutorial 3: DIA data analysis in Skyline

– by Drs. Eva Borràs & Nathalie Selevsek01:00 - 02:00 PM Lunch02:00 - 04:00 PM Selected students’ presentations and feedback by Drs.

Cristina Chiva, Eva Borràs & Nathalie Selevsek04:00 - 04:30 PM Recapitulation and evaluation


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Mr. Brendan MacLean Designation: Software Engineer & Prin-ciple Developer of SkylineInstitute: MacCoss Lab, Washington UniversityEmail: [email protected]: Mr. MacLean worked at Microsoft for 8 years in the 1990s where he was a lead developer and development manager for the Visual

C++/Developer Studio Project. Since leaving Microsoft, Brendan has been the Vice-President of Engineering for Westside Corpo-ration, Director of Engineering for BEA Systems, Inc., Sr. Software Engineer at the Fred Hutchinson Cancer Research Center, and a founding partner of LabKey Software. In this last position, he was one of the key programmers responsible for the Computational Proteomics Analysis System (CPAS), made significant contribu-tions to the development of X!Tandem and the Trans-Proteomic Pipeline and created the LabKey Enterprise Pipeline. Since August 2008, he has worked as a Sr. Software Engineer within the MacCoss lab and has been responsible for all aspects of design, development and support in creating the Skyline Targeted Proteomics environ-ment and its growing worldwide user community.Talk title: Introduction to Skyline, Statistical peak picking model, Small molecule analysis with Skyline

Dr. Cristina ChivaDesignation: Staff scientistInstitute: Proteomics Unit, University Pompeu Fabra, BarcelonaEmail: [email protected]: Cristina is a staff scientist in the CRG/UPF Pro-teomics Unit in Barcelona where her research focuses on the ap-plications of targeted proteom-

ics in projects with clinical samples. She is also involved in the development of quality control workflows in the proteomics laboratories. She holds a Ph.D. in Organic Chemistry and has done her research stages in Japan and Denmark. She has been an organizer and teacher in different courses of Targeted Proteomics and Advanced Proteomics.Talk title: Introduction to the tutorials, Quantita-tive targeted proteomics

Dr. Nathalie Selevsek Designation: Senior scientistInstitute: ETH ZurichEmail: [email protected]: Dr. Nathalie is a senior scientist at the Func-tional Genomics Center, a joint research and training fa-cility of the ETH Zürich and the University of Zürich. She

is mainly involved in the implementation and appli-cation of new quantitative proteomics workflows such as shotgun and targeted mass spectrometry-based ap-proaches. After completing her Ph.D. in biology at the Biochemical Engineering Department in Saarbrücken (Germany), she joined in 2008 the Aebersold lab for a post doctorate at ETH Zürich, where she developed targeted-MS based technologies (i.e. SRM, SWATH) for the identification and quantification of proteomes in systems biology and biomedical research.Talk title: Analyzing post-translational modifications with PRM, Introduction to data independent acqui-sition

Dr. Eva Borras Designation: ScientistInstitute: Proteomics Unit, Universi-ty Pompeu Fabra, BarcelonaEmail: [email protected]: Eva Borras joined the CRG/UPF Pro-teomics Unit after complet-ing her Ph.D. in Barcelona and post-doctorate in La Jolla, California. She is a

mass spectrometry specialist and over the last years has been involved in different biomarker discovery projects using targeted proteomics. She is an enthusi-astic teacher and helps organize the Advanced Pro-teomics Course and Targeted Proteomics Course in Barcelona, where she also gives lectures.Talk title: DIA data analysis in Skyline

Biographies


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The Targeted proteomics workshop conducted at IIT Bombay in December 2015 broadly covered the basics of Targeted proteomics experiments and included hands-on sessions on the different

modules of Skyline software.

The main objective of the workshop was to provide user interactive tutorials on several topics like Setting up a Skyline document, Preparing and exporting a transition list, Building a spectral library in Skyline, Parameter optimization, Retention time scheduling, Manual SRM data analysis, Automated Peak picking and SWATH data analysis to name a few, materials of which can be found on the skyline website.

Setting up a Skyline document- This module aims at covering the basic workflow for creat-ing a skyline document from a blank document by defining various study parameters.

Targeted Proteomics workshop-2015 at IIT Bombay


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Preparing and exporting a transition list- This tutorial covers the basics of creating a transition list.

Depending on the level of available information one can insert a transition list into Skyline, or, one can insert proteins and suited representative peptides for known targets. Building a spectral library in Skyline- This module introduces the participants to the

procedures of creating spectral libraries. Spectral libraries for SRM method design and for data analysis can be either directly added to a Skyline document or a custom library can be built from within Skyline. For the latter, data-dependent acquisition (shotgun) as well as SRM-triggered MS2 measurements, search with one of the common search engines can be used.


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Parameter optimization– This module cover topics such as Collision Energy Optimization (CEO) and Dwell time/ Cycle time which bear a lot of importance in targeted proteomics experi-ments.

SchedulingSRM-Thistutorialaimsatfamiliarizingparticipantstotheconceptofretentiontimeschedul-ingandretentiontimepredictionusingSSRCalcandiRTs.Theterm“scheduledSRM”referstomeasuringSRMtransitionsnotoverthewholechromatographicgradientbutonlyforashorttimewindowaroundapeptide’sex-pectedretentiontime.TherebythenumberofmeasurabletransitionsperSRMruncanbesignificantlyincreased.Themorepreciseretentiontimesofpeptidescanbepredicted.Anarrowerretentiontimewindowcanbedefinedandmorepeptidescanbemeasuredinasinglerunwithoutthelossofsensitivity.


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ManualSRMdataanalysis&AutomatedPeakpickinginSkyline-Thesemodulesfocusonmanualandautomatedpeakpickingwhereintheparticipantsareintroducedtotheidentificationofcorrectpeaksandmanu-allyassigningthepeaksthathavebeenmissed.AnewfeatureofSkylineusingcustompeakpickingandscoringmodelssignificantlyimprovestheaccuracyandconfidenceinthedata.Thetutorialwilltrainparticipantsincus-tomizingapeakscoringmodel,usingthemodelstoimproveSkylinepeakintegration,boundaryselectionandassigningaconfidenceleveltotheassociationbetweenthepeakanditstargetpeptide.

Thefinaltutorialon‘SWATHdataanalysisusingSkyline’coversthebasicsofpost-acquisitionanalysisforpro-teinidentificationandquantitationusingadata-independentdatasetacquiredinaQ-TOFinstrument.UsingSky-line,theacquireddatasetsforagivensubsetofproteinswillbequeried.ThesessionfocusesonsettingparametersinSkylinewhicharerequiredforthedata-independentdatasetsandfurthertheextraction


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Workshop II:MS WORKSHOP


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Preamble to the MS-Workshop

The development of soft ionization techniques have propelled the use of mass spectrometry in proteomics and with the advances in tagging strategies it has become a powerful platform for quantitative proteomics research. The emergence of LC-MS has paved a way

for a revolution in the field of proteomics. It combines the separation ability of HPLC with the superior detection ability of a mass spectrometer. The use of LC-MS has resulted in the emergence of omics approaches that have helped quantify various enzymatic activities and has led to the development of lipidomics, metabolomics and phosphoproteomics disciplines for studying and understanding biological systems. Recent studies indicate applications of iTRAQ-based LC-MS approach for quantitative proteomics, which has helped in understanding the roles of different proteins in various diseases and addressing biological questions. While there are various modifications and technicalities that make up the sophistication of the instrument, the workflows involved are extremely complex. Proteome of every organism, cell or tissue consists of thousands of proteins with wide dynamic range. For mass spectrometric analysis, it is essential to perform sample fractionation to reduce the complexity of proteins/peptides samples so that maximum number of proteins can be identified. This reduces the masking effect of highly abundant proteins/peptides and thus allows detection of low-abundant proteins. Various methods are available for sample fractionation such as strong

cation exchange (SCX) chromatography, off-gel electrophoresis, etc.

Proteomics Bootcamp is scheduled from 24th – 28th Feb, 2018. The course is structured to accommodate only 6 participants each day, to give them more personalized training right inside the newly established mass spectrometry facility at IIT Bombay (MASSFIITB). The participants will get aquainted with the basics of mass spectrometry, sample run and analysis.

MS-Workshop schedule(23th to 28th)

VENUE: ROOM NO. 304 PROTEOMICS LAB (BSBE)Time Activity Coordinators09:15 - 09:25 AM Registration & Introduction

(Group photograph)Mr. Sandip K. Patel & Dr. Akshay Bhat

09:30 - 09:55 AM Lecture 1: Instrument demo, Cali-bration

Mr. Pratip Saha

10:00 - 10:25 AM Lecture 2: LC-MS run parameters demo

Mr. Pratip Saha

10:30 - 10:40 AM Expt 1: Live session – participants 1, 2 & 3 to run sample

Mr. Sandip K. Patel

10:40 - 11:00 AM Tea break11:00 - 11:30 AM Lecture 3: Introduction to Fusion Mr. Pratip Saha11:35 - 11:45 AM Expt 2: Live session – participants

4, 5 & 6 to run sampleMr. Sandip K. Patel

11:45 - 12:25 PM Data analysis – Proteome Discover-er demo

Dr. Akshay Bhat


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12:30 - 01:00 PM Expt 3: Live session – participants to run iTRAQ or TMT samples

Mr. Sandip K. Patel

VENUE: ROOM NO. 13, VMCC (FIRST FLOOR)01:15 - 02:15 PM Lunch break; Blank run in LC-MS02:15 - 03:00 PM Lecture 4: Basics of MS-based pro-

teomics: from discovery to quanti-tation

Dr. Sanjeeva Srivastava

03:00 - 03:15 PM MS Data analysis by the partici-pants

Mr. Pratip Saha/ Dr. Akshay Bhat

03:15 - 03:30 PM Tea break03:30 - 04:30 PM Data analysis – Quantitative pro-

teomicsMr. Pratip Saha

04:30 - 05:00 PM Quiz, Feedback & Certificate Mr. Sandip K. PatelVENUE: ROOM NO. 304 PROTEOMICS LAB (BSBE)

05:00 - 05:10 PM An introduction to Targeted proteomics approaches05:10 - 05:20 PM Validation of a few target proteins in gliomas using MRM-a case study05:20 - 05:30 PM Basics of Parallel Reaction Monitoring05:30 - 06:00 PM Validation of target proteins in Meningiomas using PRM – a case study

Exploring New Dimensions in Biological Sciences using Orbitrap Fusion Tribrid Mass SpectrometerInnovation is shrinking industrial machines and medical devices to the scale of atoms and molecules. In this light, mass spectrometry will be one of the most important and versatile tools that will drive the future of biosciences through its potential utility in Research &Development wherein pharmaceutical industries too now have shifted their major focus towards the discovery of novel compounds. This technology will drive high-throughput screening of candidate molecules together with the advances in “omics” technologies (ge-nomics, transcriptomics, proteomics, metabolomics) and biomarker identification.

Mass spectrometry-based approaches are used extensively in industrial and academic fields for both routine and research purposes. With its broad range of applications in various domains like disease diagno-sis, drug discovery, environmental studies, a hands-on training on the instrumentation and applications of Orbitrap mass spectrometer becomes acutely imperative for the young researchers.

Scientists and biologists face many challenges in functional biology studies that require the study of global proteomes over many time points, precise spatial. distribution of proteins and different cellular states. These issues translate into the analytical challenge of performing reproducible and precise quantification of a few selected biological components in the presence of very complex background.

Figure 01: Orbitrap Fusion Tribrid Mass Spectrometer.


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One of the major challenges in proteomics is the quantification of low abundance proteins and pep-tides of biological relevance such as transcription factors or low stoichiometry, post-translationally modified proteins. The quantification of these analytes of interest is complicated by the very large dynamic range observed for cellular protein expression, especially in humans. With the development of next-generation mass spectrometry platforms providing high resolution and multiple detector versatility, new strategies are available to push the existing limits of quantification. The Orbitrap Fusion Tribrid Mass Spectrometer ensures that scientists do not miss anything in their area of research while building a strong platform with the combination of next-generation screening techniques and advanced targeted methods for protein quantitation. It is designed to expand researchers’ capabilities in advanced proteomics and metabolomics applications, including targeted, data-independent acquisition (DIA) and top-down analyses with the industry’s highest level of sensitivity, delivering more complete sequence coverage and allowing scientists to per-form more inclusive analyses.

This technology will drive future research and help scientists in pushing the limits of quantitation and protein characterization. It is ideal for labora-tories that require more extensive and profound analytical information from their samples, especially lower limits of detection and better sequence cover-age while characterizing proteoforms which was not possible with other high-resolution mass spectrome-try systems.

Combining Quadrupole, Orbitrap, and Ion trap mass analyzers in a revolutionary Tribrid architecture, the Orbitrap Fusion Tribrid mass spectrometer delivers unmatched analytical performance with revolution-ary depth of analysis, unprecedented usability, and exceptional robustness. Resolution up to 450,000 to remove spectral interferences CID/HCD/ETD detected by the Ion Trap or Orbitrap at any level of MSn for maximum experimental flexibility Dynamic scan management architecture lets users get maximum information from samples easily

Specifications of the Fusion mass spectrometer:- Mass RangeLinear Ion Trap and Orbitrap Mass Range:Standard–m/z50–2,000High Mass – m/z 200–4,000Orbitrap Extended Mass Range:Up to m/z 6000 without precursor ion selection

Figure 02: Orbitrap cell shown with an ion trajectory.

Figure 03: Schematic diagram of Orbitrap fusion mass spectrometer.


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Resolution15,000-450,000 (FWHM) at m/z 200 Scan RateOrbitrap MSn up to 20 HzIon trap MSn up to 20 Hz

Mass Accuracy< 3 ppm RMS using external calibration< 1 ppm RMS using internal calibration

MS/MS Sensitivity of Ion Trap2 μL of a 50 fg/μL solution of reserpine (100 fg total) injected at a flow of 500 μL/min will produce a minimum signal-to-noise ratio of 100:1 for the transition of the isolated protonated molecular ions at m/z 609 to the largest two product ions, m/z 397 and m/z 448, when the mass spectrometer is operated at unit resolution in the full-scan MS/MS mode, m/z 165–615. The test requires the HESI probe.

Dynamic Range> 5,000 within a single scan, guaranteeing specified mass accuracy

MS Scan PowerMSn, for n = 1 through 10

Thermo Scientific™ EASY-ETD™ Ion Source• Generatesfluorantheneanionsforelectrontransferdissociation(ETD)• Townsenddischargeionizationisextremelystableandrobust• Compactsize,locatedentirelywithinthefootprintoftheinstrument• Activereagentionfilteringusingmass-resolvingquadrupole

Thermo Scientific™ EASY-IC™ Ion Source• Generatesinternalcalibrantions for real-time mass calibration on every spectrum• Provides<1ppmRMSmassaccuracy

Synchronous Precursor Selec-tionUp to 15 precursors per MS2 scan, for MS3 analysis only

Multiplexing Using Ion-Rout-ing MultipoleUp to 10 precursor ions per scan using quadrupole mass filter

Polarity SwitchinOne full cycle in 1.1 sec (one full scan in positive mode and one full scan in negative mode at resolution setting of 35,000)

Figure 04: A representative schematic of LC parameters.


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Figure 05: A representative diagram showing parame-ter settings of a MS method.

Figure 06: A schematic illustration depicting MS method parameters for different applications.

Figure 07: A broad outline of different applications of mass spectrometry.

In the future, this technology will also enable scientists to:• Confidentlyquantifylowlevelanalytes,lowatomicLOQinnLCanalysisandfginhighflowanalysis• BemoreselectiveaboutwhichinstrumentstheyperformtheirMS/MSexperimentson• Characterizeintactproteinswithtop-downonLCtimescale,whichmeanslowerdetectionlimitsandhigher throughput• Elucidatestructuresmorethoroughlyandeasilybyusinganyfragmentationmode,atanystageofMSnanalysis, with detection by either analyzer, which maximizes structural information from metabolites, glycans, PTMs, and sequence polymorphism

Author - Sharad Mishra

Designation: Senior Product & Application Manager- LCMSThermo Fisher Scientific India Pvt. Ltd.First Technology Place3EPIP, Whitefield; Bangalore – 560066

Email: [email protected]

Biography: Mr. Sharad Mishra is a Senior Product & Application Manager- LCMS at Thermo Fisher. He has a vast experience working in Mass spectrometry-based plat-forms with different major Indian pharma, paint and analytical instrumentation com-

panies like Asian Paints, WATERS and Perkin Elmer over a period of 23 years. He also frequently visits many prestigious institutes and pharma industries for conducting LC /LCMS seminars, workshops and training courses.


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About the FacilityHigh Resolution Mass Spectrometry based Proteomics Research and Training Facility at Indian Institute of Tech-nology Bombay (MASSFIITB) aims to provide advanced, state-of-the-art, mass spectrometry instrumentation and support to expand omics research, education and training in India. The facility can analyze challenging low-abun-dant, highly complex samples to identify and quantify compounds in a fast and accurate manner along with a thorough elucidation of metabolite structures using the Orbitrap Fusion Tribrid Mass Spectrometer. ORBITRAP FUSION TRIBRID Ultra high mass resolution 500,000 FWHM Fast scans Multiple dissociation techniquesThe facility is open to researchers in academia, national R&D Labs, as well as corporate customers. A dedicated team of scientists will be available to help researchers in achieving their scientific goals of proteomics and metab-olomics research. During the first phase, services offered include protein identification and protein quantification (e.g. iTRAQ/ TMT/ Label-free) for proteomics analysis. During the second phase, services will be expanded to include targeted proteomics, PTM analysis, metabolomics, and other specialized applications. The facility also aims to facilitate proteomics training by conducting dedicated courses and workshops. For upcoming training programs and workshop please visit our website.SAMPLE SUBMISSION: • Pleaseregisterorloginonthefacilitywebsiteathttp://www.bio.iitb.ac.in/~sanjeeva/massfiitb/• Sampledetailsshouldbeenteredintheonlineforms• Moreinformationonhowtosubmitsamplesisavailableathttp://www.bio.iitb.ac.in/~sanjeeva/massfiitb/index.php/instructions-to-users/

MS Boot camp 10 day-workshop, 4th Dec to 15th Dec 2017 at MASSFIITB

FACILITY CONTACT INFORMATION:Prof. Sanjeeva Srivastava

Lab 304, Proteomics LaboratoryDepartment of Biosciences and Bioengineering

Indian Institute of Technology BombayMumbai – 400076, India

Telephone: +91 22 2576 7779Email: [email protected]


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Team members at MASSFIITB

Instructors:Dr. Sanjeeva Srivastava

Designation: Associate Professor and PI, Proteomics Lab, IIT BombayInstitute: IIT BombayEmail: [email protected]

Biography: Dr. Srivastava is an As-sociate Professor and Group Lead-er of Proteomics Laboratory at the

Indian Institute of Technology Bombay India, a guest professor at the Central South University, China and a Visiting Scientist at the Biodesign Institute, Arizona. He obtained his Ph.D. from the University of Alberta and post-doc from the Harvard Medical School in the area of proteomics, and has specialized expertise in applications of data-enabled sciences in global health, developing country and resource limited settings. Dr. Srivastava is recipient of several awards including the National Young Scientist Award (Canada), Young Sci-entist Awards (India) and Apple Research Technology Support Award (UK). His group is actively working in clinical oncology oriented research, focusing on two of the most commonly occurring brain cancers, viz. Gli-oma and Meningioma. The research focuses on novel biomarker identification using high-throughput pro-teomics techniques across a wide variety of platforms, including gel-based proteomics, mass spectrometry and protein microarrays. Quantitative profiling to under-stand proteome alterations along with comprehensive autoantibody profiling of serum and CSF samples in glioma and meningioma have been accomplished. His group also focuses on various neglected tropical diseases like Malaria, Dengue etc. Dr. Srivastava serves on exec-utive committee of Proteomics Society, India (PSI) and he is an active member of HUPO and US-HUPO since

2008. Dr. Srivastava had organized 6th Annual Meeting of PSI, “Proteomics from Discovery to Function” and International Conference from Dec 6th to 11th 2014 in IIT Bombay, Mumbai, and Targeted Proteomics work-shop and symposium in 10th to 14th Dec2015. This event witnessed many presidents and ex-presidents of HUPO for the first time in India. Dr. Srivastava is actively con-tributing in Editorial capacity and currently he is editor for three special issues including a “Proteomics in In-dia” special issue in Journal of Proteomics, “Proteomics research in India” in Nature India and “Protein Arrays” in Proteomics. His group has developed E-learning resources such as Virtual Proteomics Laboratory and Open Source Courseware Animations Repository as a community resource. His Proteomics video lectures (40 hours) developed by National Program on Technology Enhanced Learning (NPTEL) is freely accessible for the community. Dr. Srivastava’s teaching efforts has provid-ed him Excellence in Teaching Award in IIT Bombay, which is one of the coveted distinctions of this very prestigious institute.

Mr. Pratip Saha

Designation: Application Special-ist, Thermo Fisher ScientificEmail: [email protected]: Pratip is currently working as an Application Special-ist at Thermofisher Scientific India Pvt Ltd for the last 3 years. He has

over ten years of experience in mass spectrometry-based applications in proteomics and metabolomics. He had worked with Bruker Daltonics for four years previous-ly as Application Specialist. He obtained his M.Sc. in Biochemistry and B.Sc. in Chemistry from University

Prof. Srivastava with MS Workshop participants


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of Calcutta. He has worked in different research proj-ect of proteomics at reputed institute and Universities like Indian Institute of Science, Bangalore; Center for Cellular and Molecular Biology, Hyderabad; Universi-ty of Calcutta, Kolkata; Banaras Hindu University, Va-ranasi. During his research works, he worked on gel-based and gel-free proteomics. He is well-experienced in the labelled and label-free proteomics. In his current role, Pratip is looking after the application support for Orbitrap based omics application. He is conducting customer training, demonstration and technical discus-sion. He has delivered presentations in many national and international conferences and workshops.

MS TAs:

Mr. Sandip Kumar PatelDesignation: Doctor of Philoso-phy, Proteomics Lab, IIT BombayInstitute: IIT BombayEmail: [email protected]: Sandip Kumar Patel received his Bachelors in Zoology (B.Sc Hons.) degree from Banaras Hindu University (BHU), Varana-si in 2011 and joined Indian In-

stitute of Technology Bombay (IITB) as a M.Sc.-Ph.D. dual degree student in Biosciences and Bioengineering (BSBE) department. Currently, he is a doctoral fellow at the proteomics lab, IIT Bombay. He works on mass spectrometry based proteomics and metabolomics techniques with the aim to identify biomarkers for the disease progression in vivax malaria. He uses multiom-ics approaches for a better understanding and insight into the vivax malaria pathogenesis.

Dr. Akshay A Bhat Designation: Postdoctoral fellow, Proteomics Lab, IIT BombayInstitute: IIT BombayEmail: [email protected]: Dr. Akshay A Bhat is a postdoctoral fellow at the proteom-ics lab and his research is led by Dr. Sanjeeva Srivastava. He works as a

Bioinformatician here and his key interest are in sys-tems biology. He likes protein and gene modelling/visu-alizations through network analysis and how key mole-cules play important roles in cancers. He has completed his Ph.D. from Charite Berlin University Germany. He

has done his post-doctorate at the Vancouver Prostate Centre, where his work was focused on bladder cancer research and molecular characterization.

Mr. Yogesh Shelkar Designation: Project fellow, Proteomics Lab, IIT Bom-

bayInstitute: IIT BombayEmail: [email protected]: Mr. Yogesh Shelkar is working as a project fellow in the Proteomics Laboratory at the In-dian Institute of Technology Bom-

bay. He had worked with reputed pharmaceutical com-panies like SMTPL (P) Ltd and KDL Biotech Ltd for two years as a Microbiologist. He obtained his B.Sc. in Mi-crobiology from Pratap College and M.Sc. in Microbi-ology from Ahmednagar College, Ahmednagar. He had worked in different research projects at college level. He is well-experienced in Microbiology, Bio-safety, GLP, GMP and different quality control and manufacturing government audits. Now he is working in the High res-olution mass spectrometry proteomics training and re-search facility.

Ms. Swati Kumar

Designation: Project fellow, Pro-teomics Lab, IIT BombayInstitute: IIT Bombay

Email: [email protected]: Swati completed her BSc. in Life Sciences from St. Xavi-er’s College, Mumbai in 2014. She

then completed her Master’s in Biotechnology from DY Patil University, Navi Mumbai in 2016 and did her dissertation from National Institute of Research in Re-productive Health, Parel for a period of six months. Currently, she is working as a Project Assistant in the Proteomics Lab at IIT Bombay. She was working on us-ing mass spectrometry based approaches to study the serum proteome as well as cytokine profile of dengue fever patients to study disease pathogenesis and identi-fy early diagnostic and prognostic markers. She is now working in the High Resolution Mass Spectrometry Fa-cility based at IIT Bombay.


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Workshop-IIIINTERACTOMICS


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Preamble to the Interactomics

Economic crunches and perpetually limited educational/ research resources often make it difficult for most of the institutes to afford the sophisticated laboratory set-ups required for cutting-edge integrated omics research. Additionally, analysis and management of

large datasets obtained from the high-throughput proteomics research is also a formidable challenge and requires well-experienced personnel. Consequently, there is an urgent need for dissemination of the knowledge/experience gained by the experts of these fields to the young researchers and students. Govt. of India has approved a new program named Global Initiative of Academic Networks (GIAN) in Higher Education. GIAN has a few major objectives as; (1) to provide an opportunity for the Indian students to seek knowledge and experience from eminent international faculty, (2) to increase the participation of international students in academic institutes, (3) to create an environment for collaborative research with other foreign faculties. With this intention, GIAN has approved a course on Interactomics, to be conducted at IIT Bombay from 24th to 28th February 2018. .

The course will be co-ordinated by Dr. Sanjeeva Srivastava from IIT Bombay and Dr. Joshua LaBaer from Arizona State University. The five-day long course will have intensive lectures delivered by the course co-ordinators, in addition to talks by Dr. Ramesh Ummanni, Dr. Prasanna Venkatraman, Dr. Santosh Noronha, Dr. Sanjay Navani followed by hands-on/demo sessions for some of the interactomics courses.


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DAY-1 (SATURDAY, 24TH FEBRUARY 2018)Time Activity Details

8:15 - 8:45 AM Registrations8:45 - 9:00 AM Introduction by Dr. Sanjeeva Srivastava9:00 - 9:45 AM Lec-1 by Dr. Sanjeeva Srivastava Protein arrays for biomarker dis-

covery9:45 - 10:30 AM Hands-on session Protein Microarray

10:30 - 11:00 AM Tea Break11:00 -12:00 PM Lec-2 by Dr. Ramesh Ummanni Basics of RPPA12:00 – 1:00 PM Lec-3 by Dr. Ramesh Ummanni Applications of RPPA1:00 – 2:00 PM Lunch2:00 - 3:00 PM Lecture 4 and Demo Cell free expression arrays3:00– 4:00 PM Lecture -5 by Dr. Mukesh Jaiswal Antibody signatures defined by

high-content peptide microarray analysis

4:00 - 4:30 PM Tea Break4:30 - 5:30 PM Lec-6 by Dr. Joshua LaBaer NAPPA Technology

DAY-2 (SUNDAY, 25TH FEBRUARY 2018)TIME Activity Details

9:00 - 9:45 AM Lec-1 by Dr. Joshua LaBaer How to make NAPPA arrays: HT recombinant cloning

9:45 - 10:30 AM Lec-2 by Dr. Joshua LaBaer NAPPA – How to make NAPPA arrays: Cell-free expression system

10:30 - 10:50 AM Lec-3 Immunoprecipitation10:50 - 11:20 AM Lec-4 In-gel digestion & MS run for pro-

tein identification 11:20 - 11:40 AM Tea Break12:00 - 1:00 PM Demo session Microarray scanning, MS run1:00 - 2:00 PM Lunch2:00 - 3:00 PM Lec-5 by Dr. Saloni Sonawala Introduction to Bioprinting and

Iris™ Optical QC Benefits3:00 - 4:00 PM Lec-6 & Demo by Dr. Sivaramaiah

NallapetaBiomolecular Interaction Analytics Using MicroScale Thermophoresis

4:00 - 4:30 PM Lec-7 & Demo by Dr. Saji Menon When Protein Quality Matters: Tycho NT6

4:00 ONWARDS Tea break and cultural session (in international symposium)

Interactomics schedule(24th to 28th feb, 2018)

(Venue: VMCC IIT Bombay)


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DAY-3 (MONDAY, 26TH FEBRUARY 2018)TIME Activity Details

9:00 - 9:45 AM Lec-1 by Dr. Joshua LaBaer NAPPA based case study – breast cancer

9:45 - 10:30 AM Lec-2 by Dr. Joshua LaBaer NAPPA: case study – Tuberculosis10:30 – 11:30 AM Lec-3 by Dr. Sanjay Navani The Human Pathology Atlas: A

Pathology Atlas of the Human Transcriptome

11:30 - 12:00 PM Tea Break12:00 - 1:00 PM Demo Session Label free biosensors (SPR)1:00 – 2:00 PM Lunch2:00 – 3:00 PM Lec-4 by Dr. Uma Sinha Datta SPR session3:00 – 4:00 PM Lec-5 by Dr. Prasanna Venkatra-

manUse of SPR in Unravelling Domain Motif Interactions of Proteasomal

Assembly Chaperones4:00 – 4:30 PM Tea Break4:00 – 5:30 PM Lec-6 by Dr. Santosh Noronha

DAY-4 TUESDAY, 27TH FEBRUARY 2018)Time Activity Details

9:00 - 9:45 AM Lec-1 by Dr. Joshua LaBaer Label-free platforms – SPR & SPRi9:45 - 10:30 AM Lec-2 by Dr. Joshua LaBaer Biomarker Discovery

10:30 – 11:00 AM Tea Break11:00 - 12:00 PM Lec-3 by Dr. Sanjeeva Srivastava MS coupled Interactomics12:00 - 1:00 PM Lec-4 Biomolecular interactions using

Bio-Layer Interferometry (BLI)1:00 – 2:00 PM Lunch2:00 – 3:30 PM Hands-on session Biomolecular interactions using

Bio-Layer Interferometry (BLI)3:30 – 4:00 PM Tea Break4:00 – 5:00 PM Lecture & Demo session by Dr.

Atima AgarwalNGS Technology

5:00 - 5:30 PM Live Demo session by Mukesh Jaiswal

End to End Sample Quality Con-trol for Next Generation Sequenc-ing Library Preparation and Sure-Select Target Enrichment on the Agilent 4200 TapeStation System

DAY-5 WEDNESDAY, 28TH FEBRUARY 2018)TIME Activity Details

9:00 - 9:45 AM Lec-1 by Dr. Joshua LaBaer9:45 - 10:30 AM Lec 2 by Dr. Joshua LaBaer

10:30 – 11:00 AM Tea Break11:00 - 12:00 PM Lec-3 and Demo session by Dr.

Atima AgarwalNext-Gen Sequencing (NGS)Tech-

nology


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12:00 - 1:00 PM Lec-4 by Dr. Mukesh Jaiswa Agilent complete NGS Target Enrichment workflow for Exomes,

Targeted Panels and Beyond1:00 – 2:00 PM Lunch2:00 – 2:40 PM Lec-5 by Dr. Rahul Solanki Illumina Next Generation Sequenc-

ing- Advances and Application2:40 – 3:00 PM Lec-6 by Dr. Prashant Khedkar Helios, CyTof, Next Generation

Mass Cytometry Applications and Uses

3:00 – 4:00 PM Demo session Illumina Next Generation Sequenc-ing: MiSeq

4:00 – 4:30 PM Quiz4:30 – 4:45 PM Tea Break4:45 – 5:00 PM Concluding remarks by Dr. Joshua LaBaer and Dr. Ravi Gudi5:00 – 5:15 PM Conclusion and Certificate distribution


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Dr. Sivaramaiah Nallapeta Designation: Head Business OperationsOrganisation: NanoTemper Technologies, India Email: [email protected]

Biography: Dr. Sivaramaiah Nallapeta is Head Business Operations for NanoTemper

Technologies at Bengaluru, India. He obtained his Ph.D. in Bio-technology from Birla Institute of Technology. With more than a decade of research experience in biotechnology, molecular diag-nostics and microbiology, he has a scientific acumen and ability to manage research projects besides expediting the project goals. In this process, he has received several grants to his credit. His ex-pertise is in mass spectrometry-based characterization and use of biophysical techniques particularly MicroScale Thermophoresis (MST) for biomolecular interactions.

Talk Title: Biomolecular Interaction Analytics Using MicroScale Thermophoresis

Abstract: The analysis of bio-molecular interactions, such as pro-tein-protein, protein-nucleic acid or protein-small molecule, not only helps to develop therapeutics or diagnostics techniques, but it also provides important insights into cellular processes. Here we present the MicroScale Thermophoresis to analyze the affini-ty between biomolecules. MST analyzes the directed movement of molecules in optically generated microscopic temperature gradi-ents. This thermophoretic movement is determined by the entropy of the hydration shell around the molecules. Almost all interac-tions and also any biochemical process relating to a change in size, charge and conformation of molecules alters the thermophoresis of the molecule of interest and is thus detectable by MST.

Dr. Mukesh Jaiswal, Ph.D. Organisation: Agilent Technologies, FAS-WestEmail: [email protected]

Talk Title: Antibody signatures defined by high-content peptide microarray analysis

Abstract: Antigen arrays have been used to measure humoral immune responses. Using high-content peptide microarrays displaying overlapping peptides in the contexts of in-fectious and autoimmune diseases, allergy and cancer, have been improved the resolution of antigen arrays down to the epitope lev-el. Studies suggests that three distinct patterns of antibody reactiv-ity were identified: (i) peptides that were differentially recognized between infectious diseases-positive and healthy individuals, (ii) peptides that were exclusively recognized in all individuals with infectious diseases but not in any of the healthy ones, and (iii) pep-tides that were exclusively recognized in healthy but not infectious

diseases -positive individuals. Antibody signatures in serum from infectious diseases-positive subjects showed that IgG-defined dis-eases epitopes are very similar in individuals with different genetic backgrounds. The use of peptide microarrays is not limited to the detection of antibody signatures directed against foreign antigens in infectious diseases and allergies. Peptide microarrays displaying citrullinated peptide derivatives derived from human proteins en-abled detection of induction of antigen-specific tolerance in multi-ple sclerosis after immunization with DNA encoding myelin basic protein in a randomized, placebo-controlled, phase 1/2a clinical trial. The research used cerebrospinal fluid to probe autoantibody binding to microarray–bound peptides and demonstrated that the DNA vaccine produced cross-tolerance to other antigenic compo-nents, such as proteolipid protein. Moreover, microarrays display-ing overlapping peptides derived from autoantigens are a useful tool to detect diagnostic autoantibody signatures in autoimmune diseases such as systemic lupus erythemotosus. Peptide microar-rays can be used for the reliable detection of autoantibodies with low serum titers, such as antibodies to tumor-associated antigens in individuals with cancer. High-content peptide microarrays are a robust platform for screening entire proteomes for antibody recog-nition. This has the potential to define biologically relevant targets in the context of rational vaccine design and development of novel diagnostics.

Talk Title: Agilent complete NGS Target Enrichment workflow for Exomes, Targeted Panels and beyond.

Abstract: Next Generation Sequencing (NGS) applications are widely utilized in both basic and clinical research fields to study genomic aberrations, including SNPs, InDels, CNVs and fusion transcripts. With the widest selection of workflows and DNA/RNA target panels, Agilent Technologies is the leading provider of target enrichment products with two unique platforms: SureSe-lect and HaloPlex, cited in over 600 publications. These platforms are accompanied with Agilent’s superior solutions for whole ex-ome and whole transcriptome sequencing analysis. Agilent’s pro-vides a complete workflow for NGS library preparation with QC step. The Agilent 4200 TapeStation system allows for the analysis of samples in the Next Generation Sequencing (NGS) workflow from the starting material, through to final quality control (QC) of the DNA library prior to sequencing. The SureSelect library preparation protocol and demonstrates the performance and ap-plicability of the Genomic DNA ScreenTape, D1000 ScreenTape, and High Sensitivity D1000 ScreenTape assays in analyzing sam-ples from this workflow. It has been demonstrated in the many NGS protocols, the 4200 TapeStation system as a reliable QC plat-form for sizing and quantification analysis of the libraries. Agilent’s Hybridization-based SureSelect and PCR-based HaloPlex systems capture target regions from 1 kb to 100 Mb, with single-day work-flows from library preparation to sequencing. We have Ready-to-use catalog and custom DNA, RNA and Methylation Kits, includ-ing: SureSelect Clinical Research Exome, Focused Exome, OneSeq Constitutional Research Panel, Comprehensive Cancer Panel, and other disease-specific and methylation panels. Novel One-Seq tar-get enrichment to detect genome wide CNV changes together with

Biographies / Abstracts


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SNP/InDels in one sequencing reaction. Agilent’s Products sup-porting all NGS platforms: Illumina HiSeq, MiSeq and NextSeq; Ion Proton and PGM. This clearly demonstrates that Agilent’s pro-vides a complete workflow for NGS Target Enrichment with QC in all NGS platforms.

Talk Title: End to End Sample Quality Control for Next Gen-eration Sequencing Library Preparation and SureSelect Target Enrichment on the Agilent 4200 TapeStation System

Abstract: Introduction: The Agilent 4200 TapeStation system is an ideal QC platform for quality and quantity assessment of NGS library prepa-ration workflow solutions. The 4200 TapeStation system offers an automated electrophoresis system with rapid analysis time of 1 to 2 minutes per sample. The quality control of NGS library preparation following the NGS library preparation protocol on 4200 TapeSta-tion system with the Genomic DNA ScreenTape, D1000 Screen-Tape, and High Sensitivity D1000 ScreenTape assays.Materials and methods: Genomic DNA was extracted using the Agilent DNA extraction kit (200600). Agilent 4200 TapeStation system, Genomic DNA ScreenTape and Reagents, D1000 Screen-Tape and Reagents, High Sensitivity D1000 ScreenTape and Re-agents were obtained from Agilent Technologies. Sure Select li-brary has been prepared as per protocol provided by the vendor. All samples were run as triplicate on the 4200 TapeStation and the 2100 Bioanalyzer systems.Results and Discussion: Current NGS technologies often require the generation of short fragment libraries of the DNA that is to be sequenced. The example of an Illumina sequencing protocol de-tailed here, shows that the initial fragment size range of DNA is recommended to be between 150–200 base pairs in length. Sever-al steps were required to fully prepare the DNA for sequencing at critical steps during this workflow, ensures the success of library generation. The 4200 TapeStation system checks the integrity of the starting genomic DNA, and assesses sample quality after integrated purification steps to the final QC step prior to sequencing on the NGS platform.

Dr. Rahul Solanki Designation: Field Application Scientist

Organisation: Premas Life Sciences Pvt Ltd. Email: [email protected]: He holds Ph.D. in Molecular Biol-ogy from Jawaharlal Nehru University, India and worked at the Institute of Microbial Tech-nology, Chandigarh, India. He had extensive experience in Field of Molecular Biology in-cluding Next generation Sequencing. He has

good hands on expertise working on Illumina NGS platforms in-cluding HiseqX, Hiseq 4000/3000, Hiseq 2500, Nextseq and Miseq. He was involved in many training sessions for various types of Il-lumina library preparation and NGS run setup at various esteemed organisations.

Talk Title: Illumina Next Generation Sequencing- Advances and Application

Abstract: Next generation sequencing (NGS) is an incredibly pow-erful technology that is transforming genetics and genomics. The

concept behind NGS technology is similar to CE sequencing. DNA polymerase catalyses the incorporation of fluorescently labelled deoxyribonucleotide triphosphates (dNTPs) into a DNA template strand during sequential cycles of DNA synthesis. During each cy-cle, at the point of incorporation, the nucleotides are identified by fluorophore excitation. The critical difference between Sanger and NGS is that, instead of sequencing a single DNA fragment, NGS extends this process across millions of fragments in a massively parallel fashion.Using capillary electrophoresis-based Sanger sequencing, the Hu-man Genome Project took over 10 years and cost nearly $3 bil-lion. Next-generation sequencing, in contrast, makes large-scale whole-genome sequencing accessible and practical for the average researcher.Illumina NGS technology use an approach described as Sequenc-ing-by-Synthesis SBS. Sample libraries are created by digestion of the sample DNA, followed by ligation of Illumina specific adapters that allow capture and amplification of localized clusters suitable for imaging during each reaction cycle. Finally, the output of a se-quencing run is a bcl (base call) file that is typically converted to a FASTQ file which is a list of reads and quality scores for the confi-dence in each read.Paired-end Sequencing is typically employed with Illumina, where-by both ends of a fragment are used for sequencing, then aligning the forward and reverse data as read pairs. This not only has the benefit of doubling the number of reads without additional labour, but it also improves accuracy, alignments and indel detection. Applications of Illumina NGS include WGS, exome sequencing, targeted resequencing, metagenomics, Chip Seq, RNA-Seq, small RNA Seq etc.

Dr. Joshua LaBaer

Institute: Arizona State University, USAEmail: [email protected]: Dr. Joshua LaBaer is one of the nation’s foremost investigators in the rap-idly expanding field of personalized diag-nostics. His efforts focus on the discovery and validation of biomarkers — unique molecular fingerprints of disease, which

can provide early warning for those at risk of major illnesses, in-cluding cancer and diabetes. Formerly Founder and Director of the Harvard Institute of Proteomics, Dr. LaBaer was recruited to ASU’s Biodesign Institute as the first Piper Chair in Personalized Medicine in 2009. The Virginia G. Piper Center for Personalized Diagnostics (VGPCPD) has a highly multidisciplinary staff of mo-lecular biologists, cell biologists, biochemists, software engineers, database specialists, bioinformaticists, biostatisticians, and auto-mation engineers. VGPCPD applies open reading frame clones to the high throughput (HT) study of protein function. In addition, his group invented a novel protein microarray technology, Nucle-ic Acid Programmable Protein Array, which has been used widely for biomedical research, including the recent discovery of a pan-el of 28 autoantibody biomarkers that may aid the early diagnosis of breast cancer. He earned his medical degree and a doctorate in Biochemistry and Biophysics, from the University of California, San Francisco. He completed his medical residency at the Brigham and Women’s Hospital and a clinical fellowship in Oncology at the Dana-Farber Cancer Institute, both in Boston. He has contributed


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more than 140 original research publications, reviews and chap-ters. He is an Associate Editor of the Journal of Proteome Research, a recent member of the National Cancer Institute’s Board of Scien-tific Advisors, Co-Chair of the Early Detection Research Network Steering Committee and President of the U.S. Human Proteome Organization.

Dr. Prasanna Venkatraman

Institute: Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, IndiaEmail: [email protected]

Biography: Research Interest: Fundamental processes in normal development and in chronic diseases like cancer and diabetes

are constantly sculptured by cell fate decisions such as prolifera-tion, differentiation, cell motility and programmed cell death. Pro-teasomes play a decisive role in these processes primarily by turn-ing over the proteome landscape in a spatio temporally regulated manner. Protein Interactome Lab for Structural and Functional Bi-ology at ACTREC was established with intent to discover strategic roles played by proteasomes, in such cell fate decisions and identify new strategies and targets for intervention.

Talk Title: Use of SPR in Unravelling Domain Motif Interactions of Proteasomal Assembly Chaperones

Abstract: One of the perineal unsolved mysteries of protein-pro-tein interactions is the question of specificity. There are about 30000 proteins or nodes in the genome and if one assumes that each of them interacts with at least two different nodes then there are 60,000 independent edges (interactions). Many proteins are engaged in multiple interactions with some of them establishing as many as 100 edges. It is remarkable then how organized do-mains access their cognate interacting partners constitutively or on demand to drive specific functions. In an attempt to synthe-size a functional network from physical interactions we have used structural bioinformatics to discover novel interacting partners of PSMD9 and PSMD10. The molecular basis of interaction was char-acterized by many biophysical and biochemical approaches. In the work shop I will highlight these results and describe how Surface Plasmon Resonance is helpful in resolving the intricate details of these interactions and in designing and testing inhibitors of inter-action.

Dr. Sanjay Navani Designation: Site Director, The Human Pro-tein Atlas (HPA) Project, IndiaEmail: [email protected]

Biography: Dr. Sanjay Navani, Consultant Surgical Pathologist and Immunohisto-chemist, provides surgical pathology services through his laboratory –LAB SURGPATH.

Lab Surgpath is currently the only laboratory in the country that offers an Immunohistochemistry Stained Slide Service for more than 200 diagnostic and 20,000 research antibodies. Lab Surgpath

pathologists have contributed to The Human Protein Atlas (HPA) program by manually annotating approximately 16 million immu-nohistochemistry images over a period of eight years. The immu-nohistochemistry images form the backbone of the protein atlas. He finished his MD (Pathology) from Kasturba Medical College, Mangalore University in 1992. Subsequently, he obtained Fellow-ship in Gynecologic Pathology (1995-96) at Massachusetts General Hospital, Harvard Medical School, Boston, USA under Dr. Robert Young and Dr. Robert Scully. He set up the Immunohistochemistry Section at the Department of Surgical Pathology and Cytology at the Breach Candy Hospital Trust in 1995. He has served as a Sur-gical Pathologist and Immunohistochemist at Breach Candy Hos-pital Trust and Indian Cancer Society from 1995 to 2007. He is a Co-Founder of the Group of Gynecologic Pathologists (GGP) and a Founder Member of the Bombay Breast Group.

Talk Title:The Human Pathology Atlas: A Pathology Atlas of the Human Transcriptome

Abstract: Abstract The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human pro-teins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrom-etry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scien-tists both in academia and industry to freely access the data for exploration of the human proteome. The Human Protein Atlas consists of three separate parts, each focusing on a particular as-pect of the genome-wide analysis of the human proteins; the Tis-sue Atlas showing the distribution of the proteins across all major tissues and organs in the human body, the Cell Atlas showing the subcellular localization of proteins in single cells, and finally the Pathology Atlas showing the impact of protein levels for survival of patients with cancer. India is a major contributor to both the Tissue and Pathology Atlas for The Human Protein Atlas (HPA) Program. It is now possible to explore the genome-wide expression of individual genes in different tissues and cancers. This is largely due to large, open access platforms such as The Cancer Genome Atlas (TCGA), the Human Protein Atlas (HPA), GTEx that help accelerate our understanding of normal tissues and cancer. Studies combining resources from these platforms now show that a large fraction of human protein-encoding genes are expressed in cancer and this differential expression in many cases has an impact on patient survival. The pattern of gene expression in various cancers, their possible implications and strategies for target exploitation are discussed, as are the advantages of utilizing data and strategies from more than one large resource.

Dr. Sanjeeva Srivastava Biography: Refer to MS section


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Dr. Santosh Noronha Designation: Assistant ProfessorInstitute: Indian Institute of Technology, BombayEmail: [email protected]

Biography: Dr. Santosh Naronha completed his Bachelor’s in chemical engineering from

I.I.T Madras in 1990 and pursued his PhD from the University of Maryland, Baltimore County in 1996. He has worked as a Visiting Fellow at NIH, Bethesda and is currently an assistant professor at IIT Bombay. His areas of interest include the large scale produc-tion and purification of recombinant protein which involves vari-ous aspects such as the creation of genetic constructs, modification of host strains, optimization of fermentation and process control techniques, development of biosensors for online estimation of metabolites, and development of novel techniques for product recovery from high cell density cultures. An associated interest is the development of process techniques for large scale production of DNA vaccines. These vaccine candidates are currently the most promising methods of controlling diseases such as tuberculosis. Dr. Santosh Naronha is also involved in the application of geomet-rical mathematical techniques to protein structure analysis.

Talk Title: Multi-variate data analysis will be used to identify potential leads from microarray datasets

Ms. Saji Menon

Designation: Application ScientistOrganisation: NanoTemper Technologies, India

Biography: Ms. Menon Saji is Application Sci-entist working for NanoTemper Technologies, India since 2015 and currently responsible for support and marketing activities. With more

than nine years of research experience in biotechnology and mo-lecular biology, her expertise is in assay setup, studying interactions using MicroScale Thermophoresis and other biophysical tech-niques. She is very passionate and addresses challenges researchers were facing with goal of helping Science and Society move forward.

Talk Title: When Protein Quality Matters: TychoTM NT.6

Abstract: Tycho™ NT.6 is all about quick and precise protein qual-ity checks. Test and compare the relative quality and stability of a protein sample during any step of a purification or characteriza-tion workflow. Results are generated in three minutes using Tycho NT.6 and that means better and faster decisions can be made on the next experimental steps. The influences of buffer formulation and/or storage conditions on relative stability and similarity of ei-ther freshly prepared or batch-to batch preparations are swiftly de-termined. Tycho NT.6 automatically generates thermal unfolding profiles, identifies inflection temperatures (Ti), analyzes interac-tions effects on relative stability and monitors fluorescence sample brightness providing keen insight on sample quality and possible functionality.

Susheelendra Vaidya Designation: Field Application Specialist Organisation: Pall FortebioEmail: [email protected]: Susheelendra Vaidya is a Field application specialist at Pall Fortebio. He is experienced having more than four years in the field of label-free biomolecular interac-tion technology. He obtained M. Pharm in

Pharmaceutical chemistry from Rajiv Gandhi University of Health Sciences (2007). Having more than 9 + years industrial experience in proteomics, Mass spectrometry and label free platforms and worked at Biocon, NCBS and Water Corporation. He is currently responsible for application support, product management for Pall Fortebio products.

Talk Title: Bio-Layer Interferometry (BLI): a new tool for de-tecting Label Free Bio-molecular Interactions

Abstract: Understanding Bio-molecular interactions is a very im-portant aspect of life science research and development process. Multiple different technologies including, in-vitro Label-free an-alytical methods are used for characterization and analysis of bio-molecular interactions. Label free technologies (like BLI) provide valuable information on binding, kinetics, concentration, and the affinity of an interaction. This technique provides real-time mon-itoring of interactions between an immobilized molecule on a bi-osensor (such as a receptor) to an analyte in solution (e.g. ligand) without the need of labeling for detection. The presentation focuses on applications of BLI in a wide variety of Industrial & academic research and development environments for quantifying antibodies, proteins, small molecules and measuring their affinity and kinetics parameters in addition to specific advan-tages over traditional methodologies like ELISA & HPLC. Key words: BLI, Bio-molecular interactions, ForteBio,

Dr. Ramesh Ummanni

Designation:Institute: CSIR-Indian Institute of Chemical Technology, IndiaEmail: [email protected]

Biography: Dr. Ramesh Ummanni has worked mainly on prostate cancer related projects

identifying new potential biomarkers and understanding cell-sig-naling mechanisms driven by de-regulated proteins specifically in prostate cancer. Especially he worked with proteomics platforms for differential as well as functional proteomics. Currently, our re-search group is working on multi-disciplinary projects involving Proteomics, Signal transduction and Chemical Biology. We are focusing non-invasive biomarkers for cancer screening, Under-standing role of differentially altered protein in cancer progression by modulation of targeted protein expression using gene silencing methods. We are also actively pursuing investigations in under-standing disease mechanisms and drugable targets specific to dif-ferent solid tumors. We are searching for novel small molecules


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for modulation of drug targets relevant to cancer and tuberculo-sis. Our group is also extensively working with both in-vitro and in-vivo model systems addressing objectives from the on-going projects.

Talk Title: Reverse Phase Protein Array (RPPA) – targeted pro-teomic approach for unwiring signalling networks

Abstract: In complex diseases such as cancers, changes in protein expression and their activation by posttranslational modification are involved in tumor initiation and its progression. Often these are not reflected by genome level alterations. Therefore functional proteomics to understand altered protein functions associated with tumor development will provide insights in understanding the dis-ease pathophysiology. In functional proteomics, Reverse Phase Protein Array (RPPA) technology is useful to analyze protein ex-pression and activation in high-throughput assays on thousands of samples including tissue and cell lysates, serum, plasma or other body fluids simultaneously. RPPA can measures protein expression and its modifications such as phosphorylation. In RPPA, samples are printed on nitrocellulose coated glass slides as micro spots to accommodate large number of samples and probed with validated antibodies to analyze target of interest. RPPA requires highly val-idated antibodies Protein expression and activation data collected from limited quantity of sample allow the analysis of multiple ac-tivated signaling pathways directly and simultaneously. The power of RPPA can be useful for protein profiling, screening and valida-tion of diagnostic and prognostic biomarkers, monitoring of pro-tein kinetics, drug target identification, clinical research and indi-vidualized medicine. I will present about the RPPA technology and its high throughput applications in functional proteomics.

Uma Sinha Datta Designation: Education business managerOrganisation: Fast Trak, Lifesciences GE Healthcare Email: [email protected]

Biography: Uma Sinha Datta, PhD. acquired her doctorate degree in molecular virology from IIT Kharagpur, India, and went on to

University of Kansas Medical Center, USA to pursue her post-doc-toral research in leukemia. She published her research work in many peer reviewed journals like Blood, JBC and Journal of Vi-rology. After returning to India in 2008 she joined GE Healthcare as a senior scientist (cell biologist) eventually becoming experts in SPR (Biacore) and High content analysis (IN Cell analyzer). During this time Dr. Uma was involved in executing and manag-ing multiple projects and trainings with customers. She also holds a PMP certification from Project Management Institute, Pennsyl-vania, USA. She is currently managing the education business for Fast Trak, Lifesciences GE Healthcare, since April 2016. Dr. Uma is involved in managing and executing all technology trainings hap-pening globally for customers (both industrial and academic) on downstream, upstream bio-processing and bio-analytics. She also liaises with customers in identifying current knowledge based gaps in the market and filling them up by offering customized trainings globally.

Talk title: Surface Plasmon Resonance technology and it applica-tions

Abstract: This talk will introduce SPR technology, and the major corners stones which enables its label free and real-time interaction analysis of biomolecules. The general assay steps to run Biacore applications will be discussed which include immobilization of li-gand, sample injection and regeneration followed by the data ob-tained as sensorgram. SPR based application will be discussed with a focus on Affinity and Kinetic analysis.

Dr. Atima Agarwal

Designation: Technical Support & Lab Ser-vices ManagerOrganisation: Life sciences Solutions, Ther-mo Fisher Scientific

Biography: Dr. Atima Agarwal is working with Thermo Fisher Scientific as Technical

Support, Training and Lab Services lead. She has nearly 15 years’ experience in Life Science industry. Her current role involves ap-plication oriented training to the users on various platforms, Tech-nical Support involves providing expert guidance to the users re-garding their technical queries, planning and executing proof of concept studies. She also heads the labs providing services & and support in genomics and forensics. The job involves Designing and executing projects on advanced Ion Torrent Next Generation Se-quencing Platforms, STR genotyping, Sanger Sequencing & QPCR. She completed her masters in biotechnology from DAVV, Indore and pursued Doctor of Philosophy from AIIMS working on mo-lecular and immunological aspects of Human Immunodeficiency virus type 1 at AIIMS (All India Institute of Medical Sciences). She has been supporting Thermo Fisher Scientific’s Life sciences Prod-uct Portfolio for nearly 10 yrs.

Talk title: Expand your research with single sequencer and mul-tiple applications

Abstract: Adopting next-generation sequencing (NGS) in your lab is simpler and much more efficient than ever. Researchers have varied requirements from an NGS system which can range from sequencing a gene panel or a microbial genome today and exomes & transcriptomes tomorrow. Ion GeneStudio S5 Series with flexible chip format, accelerates the research across both small and large projects without the need to change instruments. The fast, automat-ed workflow achieves sample to answer results across a broad range of applications. With flexibility powered by the ability to choose from five Ion Torrent™ chips, these systems offer the opportunity to conduct wide-ranging experiments on a single platform. This flex-ibility ranging from 2M to 130M reads per run also means that a researcher does not have to batch samples to achieve the optimum cost efficiency. Further, the technology also provides the options of studying multiple biomarkers with minimal sample input. Ion AmpliSeq technology enables successful library preparation from challenging sample types such as formalin-fixed, paraffin-embed-ded (FFPE) tissue, retrospective samples from fine needle aspirates, and cell-free DNA (cfDNA) extracted from blood, using as little as 1 ng of input DNA or RNA to support multiple applications. All


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of this is being achieved with simple workflows with load-and-go reagents and a straightforward user interface, allowing sequenc-er setup in less than 15 minutes of hands-on time and as little as 2.5-4 hour sequencer run times. The technology addresses a major concern around NGS technology i.e. data analysis. It enables the user to go from DNA to annotated variants in a few clicks. Tor-rent Suite Software and Ion Reporter Software make it easy to get started with sequencing runs. Torrent Suite Software (pre-installed on the Torrent Server) is used to plan, monitor, track, and analyze the runs. Ion Reporter Software (cloud or local options available based on your needs) is being utilized to integrate, annotate, and interpret variants using. Since the technology offers scalability, simpler workflows, speed, ease of performing multiple applications on single system it has been widely adopted in scientific commu-nity. Ion Torrent™ technology has been referenced in over 4,000 publications to date.

Dr. Saloni SonawalaDesignation: Commercial Manager, India & Business Development ExecutiveOrganisation: ArrayJetEmail: [email protected]

Biography: Dr. Saloni is a passionate molecu-lar biologist with over 5 years of research ex-perience in personalised medicine, molecular diagnostics and cancer therapeutics from In-

dia. She soon moved over to the UK to accomplish a distinguished Business Management degree and has since, been working with several life science institutions, biotech and diagnostic blue-chip companies. Saloni has been a key member of the Arrayjet fami-ly for over 6 years, actively designing next generation microarray applications using the power of inkjet technology. As a supporting senior scientist, her primarily role has been to focus on developing and optimising wide range of scientific applications, managing as-say transfer projects and delivering advanced technical training to Arrayjet users across the globe. Her versatile techno-commercial role helped facilitate her transitioning into Arrayjet’s global busi-ness development executive in 2015. She now drives the sourcing, generating and building of new businesses for the organisation, while expanding the Arrayjet user network and implementing the capabilities of inkjet platform to different scientific sectors. She and her team consistently provide flexible custom bioprinting solutions to a diverse range of academia, research, pharmaceutical groups. Simultaneously, Saloni also serves as the commercial specialist and business manager for Arrayjet’s Indian subcontinent. Her responsi-bilities mainly revolve around executing business plans, developing strategic partnerships, directing product distributions, strengthen-ing existing project collaborations and constantly seeking perspec-tives from key opinion leaders to help shape the future of bioprint-ing. In her spare time, Saloni professionally choreographs, dances

and teaches Indian classical and Bollywood dance forms to all age groups around Scotland.

Talk title: Introduction to Bioprinting and Iris™ Optical QC Benefits

Abstract: Established since 2001, Arrayjet is UK’s leading life science company, offering innovative bioprinting solutions to researchers, pharma, drug development and clinical diagnostic groups world-wide. Arrayjet’s bioprinting platform uses a patented, non-contact, inkjet piezoelectric technology to deliver unrivalled speed, reproducibility and sensitivity with quantified precision. The non-contact technology can flexibly deposit any biological sample in chosen layout onto a selection of surfaces, faster than any other technology in the market. There are several key benefits to using the non-contact printing approach compared to traditional pin spotting technology. Arrayjet offers 5 inkjet bioprinters work-ing on inkjet technology, to drive innovative projects from R&D to commercialisation. Arrayjet Advance™ is an end-to-end CRO that offers high throughput screening solutions, custom array manu-facturing and assay development services. This unique platform supports a wide variety of applications such as biomarker profiling, small molecule screening, DNA/RNA binding, drug targeting, an-tibody validation, RPPA, glycan profiling, microfluidics and many more. Arrayjet’s bioprinting technique is multipurpose, multifacet-ed and can be implemented for majority of the scientific research applications. Arrayjet’s state-of-the-art graphical user interface, Command Centre™ Software v2.1 along with GenePix data analysis tool gives the user complete control of the assay design and data configuration. The user can easily develop their array layout within minutes, multiplex the assay and analyse data with low CV% and high reproducibility. The Iris™ Optical QC camera works in con-junction with Command Centre™ software. The Iris™ has the ability to recognise missing features within a print cycle, remember their position and reprint precious samples to deliver 100% print yield while generating real time quality control data for your novel assay. With an install base of over 100 bioprinters and nearly 300 success-ful Advance™ projects across 27 countries, Arrayjet’s unique tech-nology is tried, trusted and recommended by prime collaborators at Novartis, GSK, Johns Hopkins School of Medicine, The Sanger Institute, The Human Protein Atlas, The United States Army Med-ical Research Institute, EMBL, University of Copenhagen, Kenya Medical Research Institute, Royal Institute of Technology (KTH) and many more.


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Targeted Proteomics International Symposium


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Preamble to the International SymposiumThe Targeted Proteomics International Symposium scheduled on 25th February, 2018

is conceptualized to bring together proteomics researchers from around the world, so that participants can get abreast with the latest developments in the field of targeted proteomics. With the emergence of mass spectrometry, many powerful technologies have led to a complete face change of the discipline of proteomics, leading to a deeper understanding of biosystems at the functional level. Targeted proteomics is one such recent application of mass spectrometry which is evolving rapidly as a powerful tool to quantify proteins of interest in complex biological samples. Targeted Proteomics was declared as the Nature Method of the Year in 2012 and has now established itself as the one of the most sensitive and specific mass spectrometric analysis.

The event would be divided into five broad sessions in which several national and international scientists well-established in the field of proteomics will come together and educate the young audience with the multifarious dimensions of proteomics applications. The first session entitled “Proteomics from discovery to function” will focus on familiarizing the audience with the evolution of proteomics along with an emphasis on proteomics applications in non-clinical settings. The next session would then be taken over by interactomics and other functional proteomics studies. The highlight of the symposium will be the panel discussion which will witness joint participation from clinicians and research scientists in discussing the opportunities and challenges involved in extrapolating proteomics research to routine clinical practices from the existing laboratory conditions.

Mass spectrometry, which is the current work-horse of proteomics research, would be the focus of the third session. The fourth module will centre on the mass spectrometry-based proteomics applications in clinical studies which have come a long way from the classical gel-based approaches in global proteome analysis. The need for stringent validation and sensitive quantification leading to the development of targeted approaches would be discussed in the next session.

The last session, an amalgamation of scientific discussion and a stimulating cultural evening along with the closing remarks will conclude the event. We hope that this event will provide a suitable platform for college teachers and students for the extended interactions with the world leading proteomics scientists to build their expertise in these areas.


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08:30 - 09:00 AM Registration09:00 - 09:05 AM Invocation09:05 - 09:10 AM Opening address by Convener, Dr. Sanjeeva Srivastava09:10 - 09:35 AM Inaugural talk- Dr. Utpal Tatu, Welcome note by President PSI

SESSION 1: PROTEOMICS FROM DISCOVERY TO FUNCTIONTime Event Chairperson

09:35 - 09:45 AM Session overview09:45 - 10:00 AM Invited talk:- Dr. Niranjan

Chakraborty- Quantitative analysis of the plasma membrane proteome : A strategy for turning knowledge

into application

Dr. Gridhara Kumar Surabhi

10:00 - 10:15 AM Invited talk:- Dr. Subhra Chakraborty – ECM Proteomic Analyses of Vascular Wilt Illus-

trates Novel Regulators of Cell Wall Mediated Immunity

10:15 - 10:30 AM Invited talk:- Dr. Kalpana Bhargava – A proteomics approach to study

high altitude maladies10:30 - 10:40 AM Invited talk:- Dr. Gagandeep –

Systems biology and quantitative proteomics

10:40 - 11:00 AM Tea break (VMCC, First floor)SESSION 2: INTERACTOMICS AND FUNCTIONAL PROTEOMICS FOR HUMAN HEALTH

11:00 - 11:10 AM Session overview11:10 - 11:40 AM Plenary talk:- Dr. Joshua LaBaer –

Nucleic Acid Programmable Arrays (NAPPA) for clinical studies

Dr. Murali Chilakapati11:40 - 11:55 AM Invited talk:- Dr. Ramesh Um-

manni – Reverse phase arrays for biomarker discovery.

11:55 - 12:10 PM Industry talk:- Dr. Saloni Sonawala – Inkjet Bioprinting: A Complete

Solution For High Throughput Screening Applications

Time Event Chair person

Preamble to the International Symposium


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12:10 - 12:25 PM Industry talk:- Dr. Madhurima Kahali (Springer) – Publishing

scientific content: Manuscript, Met-rics, Ethics

Dr. Murali Chilakapati12:25 - 01:05 PM

Group discussion:- Proteomics from bench to bedside: Opportuni-

ties and challenges;

Moderators:Dr. Surekha Zingde (Proteomics

scientist)Dr. Sachin Suresh Jadhav (Clini-

cian)Panelists:

Dr. Rahul Purwar (IIT Bombay)Dr. Swati Patankar (IIT Bombay)

Dr. Sanjay Gupta (ACTREC)Dr. Jayanti Shastri (Nair hospital)Dr. Mala Kaneria (Nair hospital)

Dr. Rashmi Rana (Sri Ganga Ram Hospital)

Dr. Bhadresh Rami (SunPharma)01:05 - 01:10 PM Falicitation of morning speakers

and panelists01:10- 01:50 PM Lunch break (V.M.C.C, Ground

floor)SESSION 3: MASS SPECTROMETRY FOR CLINICAL PROTEOMICS APPLICATIONS

01:55 - 02:00 PM Session overview02:00 - 02:15 PM Invited talk:- Dr. Rapole Srikanth –

Quantitation and validation of new targets and biomarkers for multiple

myeloma

Dr. Shobhna Kapoor

02:15 - 02:30 PM Invited talk:- Dr. Suman Thakur – Mass spectrometry based quantita-

tive proteomics02:30 - 02:45 PM Invited talk:- Dr. Ravi Sirdeshmukh

– An update on HPP project and closing remarks

02:45 - 03:00 PM Invited talk:- Dr. Amol Suryawan-shi – Disease Proteome mapping

03:00 - 03:15 PM Industry talk:- Mr. Shailendra Rane – Role of nano-LC in Proteomics

SESSION 4: TARGETED PROTEOMICS RISING TIDES


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03:15 - 03:20 PM Session overview03:20 - 03:50 PM Plenary talk:- Mr. Brendan Ma-

cLean – Introduction to targeted proteomics and Skyline

Dr. Rajesh Shah

03:50 - 04:05 PM Invited talk:- Dr. Cristina Chiva – QCloud: A cloud based quality control system for the proteomics

community.04:05 - 04:20 PM Invited talk:- Dr. Eva Borràs – Tar-

geted Proteomics in clinical Re-search

04:20 - 04:35 PM Invited talk:- Dr. Nathalie Selevsek – Investigation of post-translational

modifications with PRM04:35 - 04:50 PM High Tea and Networking (VMCC,

First floor)04:50 - 05:20 PM Quiz (second floor Lecture Hall-21)

ANDProteomics Lab Tour for Speakers

05:20 - 05:30 PM Announcement of Quiz winners (VMCC Main auditorium)

SESSION 5: A STIMULATING ,SCIENTIFIC AND CULTURAL SESSION TO UNITE THE OPEN MINDS05:30 - 05:45 PM Ms. Subhra Priyadarshini – Tell me

a science story

All workshop participants are also invited

05:45 - 05:55 PM Ganesh Vandana performance by Talele sisters

05:55 - 06:10 PM Performance by flute artist – Sulei-man

06:10 - 06:30 PM Folk dances by Dr. Tushar Guha’s Nrityanjali group

06:30 - 06:40 PM Closing remarks, award & felic-itation ceremony and certificate

distribution


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Speaker: Dr. Utpal Tatu

Designation: Professor, IISc Bangalore; President, PSIInstitute: Department of Biochemistry, In-dian Institute of ScienceEmail: [email protected]

Biography: Dr. Utpal Tatu obtained his Ph.D. from Indian Institute of Science and

did his postdoctoral research at Yale School of Medicine, New Ha-ven, Connecticut. He is currently a Professor in the Department of Biochemistry at Indian Institute of Science. His research aims to de-velop cheaper and more effective medicines for neglected diseases such as malaria, giardiasis, amoebiasis, trypanosomoses and candi-diasis. Prof. Tatu has made extensive use of bio-analytical tools in-cluding mass spectrometry in his research for both proteomic and metabolomic applications. He serves as an expert panel member on United States Pharmacopeia Therapeutic Protein Panel. In addi-tion to carrying out educational workshops for various institutions, he has offered thematic workshops together with United States Pharmacopeia on bio-analytical methods for various biopharma companies. Prof. Tatu’s lab has established a successful academia–industry interaction. In addition to analyzing over two thousand challenging samples for various biopharmaceutical and pharma-ceutical industries his lab has collaborated with various national and international organizations for drug development projects and biosimilar characterization. Prof. Tatu holds international patents and is a recipient of several national and international awards in-cluding Birla science prize, Bioscience career development award from DBT and Ranbaxy Research Award, to mention a few. He is an elected fellow of the Indian Academy of Sciences and serves on the research advisory boards of several biotech companies in India and abroad. He is closely involved in advising Biopharma compa-nies about Bio-therapeutic protein characterization. Prof. Tatu is an editorial board member of Parasitology Journal published by the Cambridge Press. He has also been elected as the president of Proteomics Society of India and was formerly the Vice-President of the Indian Society for Mass Spectrometry.

Dr. Niranjan Chakraborty

Designation: Staff Scientist VIIInstitute: National Institute of Plant Genome ResearchEmail: [email protected]

Biography: Dr. Chakraborty has been honoured with ICCR Commonwealth Scholarship and Fellowship; DBT Award of Biotechnology Over-

seas Associateship; Senior Scientist, National Institute of Plant Ge-nome Research, New Delhi, 2003 to date. Dr. Chakraborty’s group has been exploring the stress-responsive organelle proteomes of economically important crop species for greater understanding of the molecular mechanisms of stress tolerance. Indeed, India’s first mass-spectrometry-based plant proteomics paper came from his

laboratory. The knowledge of the stress-responsive protein reper-toire would contribute in understanding the role of differentially regulated proteins and/or their post-translational modifications. Therefore, the major focus has been to identify the dynamics of stress-responsive proteins (SRPs), which would not only aid in elucidation of the mechanism underlying stress tolerance, but also serve as a valuable inventory for crop improvement program.

Talk title: Quantitative analysis of the plasma membrane pro-teome: a strategy for turning knowledge into application.

Abstract: Plasma membrane (PM) encompasses total cellular con-tents, serving as semi-porous barrier to the cell exterior, which regulates the cellular exchanges in a spatiotemporal fashion. Most of the essential tasks of PMs including molecular transport, signal transduction and cell-cell interactions are carried out by their pro-teinaceous components, which make the PM protein repertoire to be diverse and dynamic. To dissect the molecular basis of adapta-tion, we developed the dehydration-responsive PM proteome map of a grain legume, chickpea. An inventory of 2732 proteins, the largest in any crop species thus far, was created, of which 163 pro-teins were identified as dehydration-responsive. A critical screen-ing of the molecular signatures in the proteome landscape led to the identification of an integral PM protein harboring an EF-hand domain flanked by two Na+/Ca2+ exchanger domains. The trans-porter was found to be consistently downregulated, at the levels of both protein abundance and mRNA expression. To probe its reg-ulatory role, we generated overexpression (OE) lines of the candi-date gene under RD-29 stress inducible promoter. When subjected to dehydration, the overexpression line showed significant loss of vigour as compared to the unstressed control. Furthermore, the overexpression lines were found to be compromised in photosyn-thetic activities and hypersensitive to oxidative stress. These results may help in understanding the spectrum of plasma membrane proteins and the biological processes they control for enhanced stress tolerance in legume in specific and plants in general.

Dr. Subhra Chakraborty Designation: Staff Scientist VIIInstitute: National Institute of Plant Genome Research.Email: [email protected]

Biography:Subhra Chakraborty, received her Ph.D. from Jawaharlal Nehru University, New Delhi, India and did Visiting Scientist work

at Yale University, USA. She is currently a Professor at National Institute of Plant Genome Research (NIPGR), New Delhi, India. She has been instrumental in initiating and establishing Plant Pro-teomics and Translational research in India and contributed sig-nificantly in the basic and applied bio-technology. The central aim of her laboratory is to elucidate the molecular mechanism, pro-teomic pathways, and metabolic fingerprints involved in nutrient- and stress-response and to identify key genes for modifying such

Biographies / Abstracts


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traits. She has several publications in internationally reputed jour-nals, international patents and awards. She has been serving as an editorial board member and reviewer to a number of National and International journals. She is a Fellow of three National Science Academies in India, IAS, NASI and NAAS. She is Vice President, PSI; Council Member & Country Representative, AOAPO; Elect-ed Council Member, HUPO; Member, INPPO; Member, ACS; Life Member, SBC, India; Life Member, ISCB; Life Member, ISTR. She has mentored more than fifty Ph.D., post-doctoral, undergraduate students.

Talk title: ECM Proteomic Analyses of vascular wilt illustrates novel regulators of Cell wall mediated Immunity

Abstract: Morbidity and mortality associated with fungal infec-tions and emergence of resistant fungal strains necessitate study of fungal pathogenesis and host innate immunity. Innate immune response is governed by genotype-dependent conserved cellular events. However, the underlying molecular mechanism by which this process is regulated against fungal pathogen is less explored. Fusarium oxysporum, a medically and agronomically important pathogen is known to be associated with vascular wilt in plant. Wilt disease is a major impediment for global chickpea produc-tivity. To elucidate regulatory framework of Fusarium-associated disease and immune response, we analyzed the gene and protein expression during infection, integrated temporal expressions and network analysis in chickpea. Temporal proteome and metabo-lome was developed with ECM enriched fraction using quantita-tive 2-DE and iTRAQ coupled ESI-MS/MS and Triple-TOF/MS and GC-MS analyses, respectively. Longitudinal spatiotemporal multiomics analyses and the derived biomolecular networks re-vealed organ and organelle function in contrasting genotypes during fungal invasion. Network analysis identified major protein hubs enriched in known and novel disease and immunity-relat-ed prognostic proteins pointing towards the onset and context of disease signaling and metabolic pathway activations. Finally, this study for the first time provides novel insights on host-specific im-mune signaling that impinge upon the surveillance mechanism of innate immunity in Fusarium-associated disease.

Dr. Kalpana BhargavaInstitute: DIPAS, DRDOEmail: [email protected]: Dr. Kalpana Bhargava completed her Ph.D. in Peptide Chemistry from Banaras Hindu University in a joint collaboration with Indian Institute of Science, Bangalore in 1999. After her Ph.D. she perused 10 years of multi-disciplinary research in academics and R & D

environment from USA. Dr. Bhargava joined DIPAS, DRDO, Del-hi in April 2008. As scientist in Defence Institute of Physiology & Allied Sciences (DIPAS), she is heading the Division of “Peptide and Proteomics”. She has twenty five years of research experience in a wide range of areas which includes: anti-oxidant peptides, an-ti-microbial peptides, free radical biology, mitochondrial biology, nano-conjugate chemistry, protein biochemistry, proteomics, ribo-somal biology and synthetic medicinal chemistry. She has almost 65 international, peer reviewed journal publications, one book, two book chapters, three patents and several scientific awards/hon-

ours to her credit. Her current research work includes, proteome profiling of plasma/serum exposed to hypoxia at high altitude and Nano-material application for maladies caused at extreme environ-ment and drug delivery.

Talk title: A proteomics approach to study high altitude mala-dies

Abstract: Hypobaric hypoxia is caused by reduced barometric pressure resulting in arterial hypoxemia even though fraction of inspired oxygen (FiO2 20%) remains unchanged. This challenges the human physique and psyche, especially when, people from plains (<1500 m) ascend to an altitude beyond 2500 m at a rapid rate, culminating in several ailments and in worst-case scenario, death. Although these ailments are cured by early descent, they are lethal without medical aid. Hypobaric hypoxia, by reducing the available electron acceptor (oxygen) in respiratory chain, causes ample redox stress at appropriate altitude and duration to cause life threatening conditions like Acute mountain sickness (AMS), High altitude pulmonary edema (HAPE) and High altitude cerebral ede-ma (HACE). These diseases potentially affect millions visiting high altitude areas every year. Although many interventions are avail-able for preventing high altitude illness, the protein networks that are affected by them or help evade them during hypobaric hypoxia exposure are not properly elucidated causing the known interven-tions to cause side-effects and require medical supervision. In a nutshell, these interventions provide symptomatic relief but can’t confer acclimatization. Thus there is an urgent requirement to ad-dress the issue of hypobaric hypoxia at the proteome level and pro-vide suitable interventions based on the protein networks involved in AMS, HAPE and HACE. Over many years, we have amalgam-ated considerable insight into the different networks affected by hypobaric hypoxia across humans (in plasma and recently, salivary proteome) and animal model.

Dr. Ramesh UmmanniBiography: Refer to Interactomics .

Talk title: Reverse phase arrays for biomarkers discovery.

Dr. Gagan Deep Jhingan

Designation: Scientist Organization: VproteomicsEmail: [email protected]

Biography: Dr. Gagan Deep Jhingan complet-ed his Masters and Ph.D. in Biotechnology from Jawaharlal Nehru University. He has

worked as Wellcome/DBT Early Career Fellow at National Insti-tute of Immunology, New Delhi (2010-15) and was a visiting guest researcher at Prof. Ruedi Aebersold Group, ETH, Zurich. He has started Valerian Proteomics Company based in Green Park, New Delhi to provide high end Discovery and Targeted proteomics ser-vices to researchers.


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Talk title: Systems Biology and quantitative proteomics

Abstract: Quantitative proteomics is a powerful approach used for both discovery and targeted proteomic analyses to understand global proteomic dynamics in a cell, tissue or organism. Label-free strategies are also available for both relative and absolute quan-titation. Although these strategies are more complex than mere protein identification, quantitative proteomics is critical for our understanding global protein expression underlying the molecular mechanisms of biological processes and disease states.

Dr. Joshua LaBaer Biography: Refer to Interactomics section

Talk title: Nucleic Acid Programmable Pro-tein Arrays (NAPPA) for clinical studies

Dr. Saloni Sonawala Biography: Refer to interactomics section

Talk title: Inkjet Bioprinting: A Complete Solution For High Throughput Screening Applications

Abstract: Established since 2001, Arrayjet is UK’s leading life science company, offering innovative bioprinting solutions to research-ers, pharma, drug development and clinical

diagnostic groups world-wide. Arrayjet’s bioprinting platform uses a patented, non-contact, inkjet piezoelectric technology to deliver unrivalled speed, reproducibility and sensitivity with quantified precision. The non-contact technology can flexibly deposit any bi-ological sample in chosen layout onto a selection of surfaces, faster than any other technology in the market.Arrayjet offers 5 inkjet bioprinters working on inkjet technology, to drive innovative projects from R&D to commercialisation. Ar-rayjet Advance™ is an end-to-end CRO that offers high throughput screening solutions, custom array manufacturing and assay devel-opment services. This flexible platform supports a wide variety of applications such as biomarker profiling, small molecule screen-ing, DNA/RNA binding, drug targeting, antibody validation, RPPA, glycan profiling, microfluidics and many more. Arrayjet’s bioprinting technique is multipurpose, multifaceted and can be implemented for majority of the scientific research applications.With an install base of over 100 bioprinters and nearly 300 success-ful Advance™ projects across 27 countries, Arrayjet’s unique tech-nology is tried, trusted and recommended by prime collaborators at Novartis, GSK, Johns Hopkins School of Medicine, The Sanger Institute, The Human Protein Atlas, The United States Army Med-ical Research Institute, EMBL, University of Copenhagen, Kenya Medical Research Institute, Royal Institute of Technology (KTH) and many more. Arrayjet’s high throughput screening solutions, enable researchers to accurately analyse tens and thousands of samples by effectively

generating over 2 million data points in every assay. High-density multiplexing allows complex molecular interactions to be charac-terised at a much faster rate. Arrayjet bioprinting offers all benefits of laboratory automation while significantly conserving precious samples, enhancing assay sensitivity, minimising operational costs and overall delivering a complete solution for your novel research projects.

Dr. Madhurima Kahali

Designation: Associate Editor, Springer (a part of Springer Nature)Organization: Springer (a part of Springer Na-ture)Email: [email protected]

Biography: Dr. Madhurima Kahali is a Publish-ing editor, in the Biomedicine unit of Springer Research Group. She is currently based out of New Delhi. She holds a Master’s degree in Plant Biology from Calcutta University; and a PhD in Genetics, from the University of Delhi South Campus. She has been working with Springer Nature, since 2015. At Springer, she is responsible for developing and managing the Biomedicine portfolio of books and journals. She has also launched two new book-series for Springer. She is a voracious reader, and has a strong interest in the latest de-velopments in science & technology.

Talk title: Publishing Scientific Content: Manuscript, Metrics, Ethics

Abstract: Your research is never complete, unless, you publish the results of your experiments. Publishing is an integral step in the re-search lifecycle and in your career progression, as a scientist. Pub-lication is a multi-step process, involving- design of experiments, literature review, putting together a manuscript, and finding the most suitable journal for your article. Another good way to publish your research, and elaborate on your area of interest, is to venture into book publication. This talk would introduce you to Springer Nature, a leading STM publisher for 175 years, and home to many of the world’s foremost researchers, including more than 200 Nobel laureates. The talk will not only take you the workflow and timeline of publication, it will also give you insights into sharing your re-search post-publication. Apart from publication, the talk will brief-ly touch upon the interesting areas of search engines to search for the latest research; various metrics to gauge the reachability of your publications; the different business models for journal; publishing ethics; content sharing etc. The concise talk should give you a bird’s eye view of STM Publishing.

vDr. Surekha Zingde

Designation: Dy. Director, (Retired) and President, PSIInstitute: ACTREC, Tata Memorial CentreEmail: [email protected]

Biography: Dr. Zingde retired as Dy. Direc-tor, Cancer Research Institute, ACTREC,


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Tata Memorial Centre, Kharghar, Navi Mumbai, in March 2013 after 33y service with the Centre. She is presently the President of Indian Women Scientists Association (IWSA). Her expertise is in Cancer Biology, chronic myeloid leukemia, membrane proteins and signal transduction with present interest in Oral cancer pro-teomics. She was Professor of Life Sciences of the HBNI. She is Chairperson of the Indian Scientific Advisory Committee of Lady Tata Memorial Trust. She is a reviewer for several journals and re-viewer of thesis from different universities. She is a member of the Scientific advisory committees and Chairperson of the ethics com-mittees of different institutions. Surekha has been a visiting faculty at University of Mumbai-DAE-CBS, a member of the Research and Recognition Committee of ICT, Mumbai and member of govern-ment project review and funding committees. She has vast experi-ence in setting up a Research Institute. She provides consultancy for life science research. She is the immediate past President of the Proteomics Society, India. She has 75 peer-reviewed papers, several book chapters, a monograph and 4 patents.

Dr. Sachin Suresh Jadhav

Designation: Consultant Hematologist & BMT PhysicianInstitute: Fortis Hospital, BangaloreEmail: [email protected]

Biography: Dr. Sachin Suresh Jadhav works as a Consultant Hematologist and BMT Physi-cian at BGS Global Hospital, Bangalore. He

completed his MBBS from the Mumbai University. He has also pursued his MD in General Medicine and did his DM in Clini-cal Hematology. Dr Sachin has a Fellowship in Leukemia from the University of British Columbia. He has a special interest in Hema-tology and Pathology. Dr. Sachin is completely passionate about his work. Dr. Sachin has written many papers and abstracts which has been published in various international as well as national jour-nals. He has carved a space for himself in all the institutions he has worked in. He has proven to be capable of handling stress and deals with complicated cases in the most skillful manner.

Dr. Rahul Purwar

Designation: Assistant Professor and Princi-ple Investigator Immunoengineering Lab, IIT BombayInstitute: IIT BombayEmail: [email protected]

Biography: Rahul Purwar has completed his Ph.D. from Hannover Medical School, Hannover, Germany and postdoctoral studies from Harvard Medical School, Boston, USA. He has worked for an Oncology company, ImmunoGen Inc. Waltham, USA before returning to India to join IIT-Bombay as an Assistant Professor. He has published several papers in reput-ed journals and has received many awards. His research is main-ly focused on Cancer immunotherapy which is an emerging and a transformative approach for the treatment of cancer patients

through personalized approaches. Cancer of each patient is unique and personalized approach would be an ideal for successful cancer treatment: engineering immune-system that target antigen specific to each patient. His work involves combining Adoptive T cell ther-apy with engineered autologous T cells for patients. His research also has shown that treatments with engineered CAR-T cells can be beneficial for acute lymphocytic leukemia patients and chronic lymphocytic leukemia (CLL) patients.

Dr. Swati PatankarDesignation: ProfessorInstitute: IIT BombayEmail: [email protected]

Biography: Dr. Swati Patankar is a professor at the department of Biosciences and Bioengi-neering, IIT Bombay since 2003. She complet-ed her Ph.D. in molecular Biology in 1996 and was a post-doctoral fellow at Immunology and

Infectious diseases at Harvard School of Public Health, Boston, USA. She is the group head of molecular parasitology laboratory at IITB and currently studies how Malaria parasite regulates the expression of its genes. Her lab. Brings together strengths in mo-lecular biology and bioinformatics with a long term goal of finding parasite- specific pathways that might be targets for therapeutic intervention. Her research interests includes studying the regula-tion of gene expression in the malaria parasite, Plasmodium falci-parum, bioinformatics analysis of P. falciparum genome sequence to study regulation of gene expression and acquisition of genetic diversity, P. falciparum tubulin a target for anti-malarial how the malaria parasite regulates the expression of its genes. Her research interests include studying the regulation of gene expression in the malaria parasite P. falciparum, bioinformatics analysis of p. falci-parum genome sequence to study regulation of gene expression and acquisition of genetic diversity.

Dr. Jayanti Shastri Designation: ClinicianHospital: NAIR hospitalEmail: [email protected]

Biography: Dr. Jayanthi Shastri is currently a Professor & Head of Microbiology, TNMC and BYL Nair Ch. Hospital. On completion

of MD in Clinical Microbiology, Dr. Shastri pursued her interests in Infectious disease diagnosis with special reference to validating new and rapid diagnostic techniques for Dengue, Malaria and HIV. Dr. Shastri planned and commissioned a state-of-the-art molecu-lar diagnostic facility at the infectious disease hospital in Mumbai. Her laboratory is recognized by the National AIDS Control Or-ganization as “Regional HIV Reference laboratory” for conduct-ing HIV viral loads by real time PCR and early infant diagnosis by DNA PCR. She has authored several articles in national and inter-national peer-reviewed journals. Dr. Shastri was funded “Visiting scientist” at Albert Einstein College of Medicine (AECOM,), New York, USA in 2009 under AIDS International Training program


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(AITRP). She was also a recipient of CFAR grant from AECOM to conduct “A pilot study of HIV among women attending a health clinic in Mumbai”. In October 2015, she have received “Teaching Professorship” award from American society of Microbiology to teach Infectious diseases at University of South Florida.

Dr. Mala KaneriaDesignation: ClinicianHospital: NAIR hospitalEmail: [email protected]

Biography: Dr. Mala V. Kaneria is a Professor and Unit Head of the Department of Medicine at T.N. Medical College and B.Y.L. Nair Ch. Hospital. Dr. Mala heads the Geriatric OPD in

TNMC and BYL Nair Ch. Hospital. Her special interests include Infectious Diseases and Tropical Medicine. She is a Member of Advisory Board of Journal of Association of Physicians of India (JAPI) and an Ex Guest Editor of The Journal of General Medicine. She is a Member of Hospital Infection Control Committee (HICC) at TNMC and a member of AIrborne Infection Control Commit-tee. She has been teaching UGs, PGs, dental students for over 22 years and has guided more than 15 PG students with their disserta-tion. She has authored more than 70 publications and is the recip-ient of several awards. In 2009, she was awarded the Fellowship of The Indian College of Physicians by the API in 2009 and M.J. Shah Award – “To evaluate the levels of Procalcitonin in febrile patients” at the APICON 2010 held at Jaipur among several others.

Dr. Sanjay GuptaDesignation: Principal investigator, TMC- ACTRECInstitute: ACTREC, Tata Memorial CentreEmail: [email protected]

Biography: Dr. Sanjay Gupta received his Ph.D. in 1995 from Biochemistry and Mo-lecular Biology Group, Banaras Hindu Uni-versity, Varanasi and performed postdoctor-

al work with Prof. M.S. Kanungo at the Institute of Life Sciences, Bhubaneswar and Banaras Hindu University, Varanasi. Dr. Sanjay joined Cancer Research Institute, Tata Memorial Center, Mum-bai in 1999. Dr. Sanjay Gupta is a principal investigator at the TMC-Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India A major research interest in his lab is to understand the epigenetic changes that take place at the molec-ular level during different stages of malignant transformation and DNA repair per se. Recently; we have uncovered an alteration of histone variants in initiation and progression of hepatocarcinogen-esis. Current goals of the lab are to understand (1) how different alteration in histones in specific cell cycle stage affects their role in DNA damage response that escort repair machinery proteins in and out of the chromatin (2) transcriptional regulation of histone variants, variant-specific PTMs and their binding partners during carcinogenesis (3) how structure and function of chromatin fiber is altered when the canonical histone is replaced by histone variant and (4) how all these alterations can be used for better treatment modalities.

Dr. Rashmi RanaDesignation: Assistant Professor, GRIPMERInstitute: Sir Ganga Ram Hospital, New DelhiEmail: [email protected]

Biography: Dr. Rashmi is working as an Assis-tant Professor in the Department of Research in Sir Ganga Ram Hospital (SGRH), New Delhi, India. Her research interests lies in the identifi-

cation of protein-based biomarkers for early diagnosis / post-treat-ment surveillance and therapeutics of brain tumor (Glioma) and biliary tract cancer. She completed her Ph.D. from NIOP, Indian Council of Medical Research (ICMR), New Delhi, India in Novem-ber 2012 after which she worked as a Postdoctoral Fellow in All India Institute of Medical Sciences (AIIMS), New Delhi, India. She has also worked as a Research Associate III in Defense Institute of Physiology and Allied Sciences, DRDO, Delhi, India. Additionally, she has several awards to her credit namely; “International Travel Grant from Department of Science and Technology (DST), Min-istry of Science and Technology, Government of India” in 2010, Research Student Award of Society of Toxicology PPTOXII confer-ence held in Miami FL, U.S.A, Dec 2008, Student Award of Air Pol-lution and Health conference held in San Diego, California, U.S.A, March 2010 and Fast Track young scientist by Ministry of Science and Technology, DST, Government of India in 2014.

Dr. Bhadresh Rami:Email: [email protected]

Biography: Dr. Bhadresh Rami holds a Ph. D in Biochemistry and Biophysics from the pres-tigious National Center for Biological Sciences, Tata Institute of Fundamental Research, Banga-lore. His seminal work on Protein Folding and

Unfolding pathways led to the discovery of key intermediates on the folding pathway and a detailed characterization of the transi-tion state of Protein Folding. He moved to the world renowned, Department of Biochemistry, Stanford University School of Med-icine in the laboratory of Prof. James A. Spudich for his Post-doc-toral research. His work provided key evidence on the presence of flexible elements in the structure of Myosin VI that modulated the mechano-chemistry and enabled it to take long and diffused steps along actin filaments. Following his post-doctoral tenure, Dr. Bhadresh Rami decided to apply the fundamental understanding of biology at the molecular level in the field of Drug Discovery in Biopharma industry in San Francisco and subsequently moved to his home country, India. He has served in increasingly senior roles in start-up, mid-size and large global multi-national drug discov-ery companies in the field of small molecule drug discovery. His areas of research include in-vitro studies related to mechanisms of origin and progression of human diseases and screening of small molecules in the fields of oncology, cardio-metabolic, inflamma-tion, obesity, diabetes, pain and neuro-degenerative diseases. He is a recipient of several awards and fellowships and a member of the American Chemical Society (ACS) and American Association for Advancement of Science (AAAS). He has a keen interest in ed-ucation and acts as a reviewer of post-doctoral fellowships for the Marie Curie Institute; is on the Board of Studies and reviewer of Research plans for colleges and Universities in India.


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Dr. Rapole SrikanthDesignation: Faculty ScientistInstitute: National Centre for Cell Science, PuneEmail: [email protected]

Biography: Dr. Srikanth Rapole completed his master’s degree in organic chemistry from Devi Ahilya University. He did his Ph.D. in analyti-cal chemistry from Indian Institute of Chemi-

cal technology (IICT), Hyderabad where he developed new mass spectrometry methods for analysing beta-carbo-peptides. He did his post-doc from University of Massachusetts (UMASS) on met-al-protein interactions and protein-protein interactions to under-stand the mechanism of protein aggregation and amyloid forma-tion. After that, he worked as proteomics and mass spectrometry lab director for two years at University of Connecticut. Currently, he is working as a scientist at NCCS, Pune. He is an active member of Indian society for mass spectrometry, American society for mass spectrometry and proteomics society of India. He has published more than 50 publications in reputed international journals.His main research interest is to investigate biomarkers and thera-peutic targets for various cancers using state-of-the-art and high-ly sensitive mass spectrometry-based proteomic approaches. His group also investigating phosphoproteomic profiling and changes in phosphorylations for various cancers to understand phosphory-lation mediated signalling pathways. In addition, his group is work-ing to identify and quantify key metabolites and lipids associated with various cancers using mass spectrometry and bioinformatics.

Talk title: Quantitation and validation of new targets and bio-markers for multiple myeloma

Abstract: Multiple myeloma (MM) is a heterogeneous disease and accounts for 14% of all hematological malignancies. In MM, ma-lignant plasma cells expand and accumulate in the bone marrow, leading to bone resorption and the over production of antibodies. The major challenge remains the identification of better prognos-tic and therapeutic biomarkers. In this work, we used MM serum, Bone marrow interstitial fluid (BMIF), BM mono nuclear cells and respected controls. Proteins from Serum, BMIF and BM Mono nu-clear cells (MNCs) were extracted and differential proteomic anal-ysis was performed using 2D-DIGE, 4-plex iTRAQ and SWATH. In the study of serum proteome alterations in MM, our quanti-tative proteomic analysis resulted in 140 differentially expressed proteins of which 51 proteins showed increased expression and 89 proteins showed decreased expression. In BMIF study, we identi-fied 184 differentially expressed proteins out of which 101 proteins were up-regulated and 83 proteins were down-regulated. Further, proteomic analysis of BM MNCs yielded a total 892 proteins us-ing SWATH analysis in which 222 proteins were statistically dif-ferentially expressed. Bioinformatics data suggest that DNA rep-lication, angiogenesis, apoptosis, integrin, WNT, CCKR signalling pathways were altered in MM. Validation results in a new cohort of samples using western blot and MRM are consistent with quan-titative proteomics data. Based on the literature, we selected three proteins viz. Plasma cell induced resident E.R protein (MZB1), Voltage dependant anion channel 3 (VDAC3), Cullin associated and neddylation dissociated 1 (CAND1) for further functional

studies. These proteins signature are not only helpful as diagnos-tic and prognostic markers but also provide insights into disease pathogenesis information of MM.

Dr. Suman ThakurDesignation: Senior ScientistInstitute: Centre for Cellular and Molecular Biology, HyderabadEmail: [email protected]

Biography: Dr. Suman Thakur has worked on Mass Spectrometry with Prof. P. Balaram at Molecular Biophysics Unit (MBU), Indi-an Institute of Science (IISc) Bangalore and

on High throughput Quantitative Proteomics with Prof. Matthias Mann at Max Planck institute of Biochemistry (MPIB), Munich, Germany. Currently his lab at CCMB Hyderabad focuses on ap-plication of Mass Spectrometry in Health and Disease especially target to Drug Development. His group uses mass spectrometry based high throughput quantitative proteomics, natural product chemistry, cell biology, animal model, stem cells and modern biol-ogy approach to find the target, develop novel drugs and elucidate its mode of action against cancer and other metabolic disorders such as diabetes. Cancer is a hyperplastic condition that leads to uncontrolled proliferation, invasion, metastasis, dysregulation of apoptosis and cell cycle. Cancer is the second leading cause of worldwide human mortality after cardiovascular diseases. Dr. Su-man Thakur’s lab is involved in investigating the efficacy of various natural metabolites on different human cancer cells like leukaemia, melanoma, and lung cancer. Further, the molecular basis for EGFR associated cancer progression, response and resistance to EGFR targeted therapy in lung cancer, and other cancers has also been investigated.

Talk title: Mass spectrometry based quantitative proteomics

Abstract: Quantitative proteomics has great potential to uplift the human health care especially to diagnose the disease at ear-ly stages and help in the treatment of disease. We have developed a single-run analysis technique without any pre-fractionation to understand and quantify accurately the changes at the level of proteome, especially with very low amount of sample. It has great potential in early diagnosis of the disease where multiple biomark-ers need to detected simultaneously and also in the detection of post-translational modifications. In depth quantitative proteomics should able to find the cause of disease, especially narrowing down to particular gene and it is coming almost closer to transcriptom-ics and genomics. The quantitation of proteins using stable isotope labeling with amino acids in cell culture (SILAC), Isobaric tags for relative and absolute quantitation (iTRAQ) and label free quan-titation (LFQ) has been applied to find the biomarkers especially in infectious disease, metabolic disorder-diabetes and its compli-cations and pre-eclempsia/ gestational hypertension. Mode of ac-tion and signalling mechanism of the known and novel drugs has been revealed by using quantitative proteomics. It is very helpful to understand the host-pathogen interaction including complex process of their signalling mechanism. Our group is working to develop novel anti-cancer drug targeting Cell adhesion, AKT sig-naling and EGFR against different specific cancers such as retino-


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blastoma, melanoma, leukaemia and lung cancer using cell culture and mouse model including xenograft, orthotopic and knock out, along with the help of quantitative proteomics.

Dr. Ravi Sirdeshmukh Designation: ScientistInstitute: Mazumdar Shaw Centre for Translational Research, Institute of Bioin-formatics, HyderabadEmail: [email protected]

Biography: Dr. Ravi Sirdeshmukh did his Ph.D. in Biochemistry from the Center for Cellular and Molecular Biology (CCMB),

Hyderabad – a premier national laboratory. He also worked as a post-doctoral visiting associate at the Washington University Med-ical School, St Louis, MO, and a visiting Scientist at the National Institute of Health, USA. He worked at the CCMB for more than 2 decades, was holding the position of Director-Grade Scientist and heading the Proteomics Lab before joining the Institute of Bioin-formatics as Distinguished Scientist. He now holds a joint appoint-ment as Principal Advisor, Neuro-oncology Research at MSCTR. His research interests span in the areas of protein and nucleic acid biochemistry and his earlier work included RNA processing, mRNA stability, structure-function relationship of ‘ribonucleases’ and their regulation. More recently his interests have been in the areas of Proteomics of gliomas – a major class of brain tumors and Head & Neck cancers. At the CCMB, he had been the nodal sci-entist in CSIR network programs in Proteomics and also served as the Consortium Manager in CSIR Proteomics Network for In-ternational Collaborations. He is also associated with some of the International research initiatives in Proteomics such as Membrane Proteomics Initiative of AOHUPO and the ongoing Chromosome Centric Human Proteome Project initiated by HUPO. He is an ex-pert reviewer for International Proteomics journals, a member of the Editorial Board of the International Journal of Proteomics and Bioinformatics. Ravi Sirdeshmukh serves on the research adviso-ry panels of several Institutes and Centers in India and that of US Pharmacopeia for protein therapeutics. He is an elected member of the council of Human Proteome Organization (HUPO) and Asian Oceanian HUPO. He is the founder President of the Proteomics Society, India which is strongly dedicated to Proteomics Education and has played an important role in educational activities in pro-teomics in India through a large number of invited lectures, or-ganization of training workshops, International Proteomics Con-ferences and Discussions. He has trained and mentored a number of young associates, Ph.D. students and post-doctoral fellows. At MSCTR, he is spearheading translational research programs in brain tumors.

Talk title: Proteomic changes in Glioblastoma: Taking them to Clinical Application

Abstract: A major application of Proteomics is to understand dis-ease biology, cancer being one of the most widely targeted disease. Our interest has been to study proteomic changes in Glioblastoma (GBM)- the most common, aggressive and lethal form of primary

brain tumors, to understand tumor-associated processes, path-ways and networks and their regulation. One approach would be to pick a single molecule of functional importance from the pro-teomic analysis results and investigate it further using cell models. One example is : GPCR 56 – a novel receptor , identified from the proteomic analysis being studied as a drug target. However, to make sense out of larger repertoire of molecules requires a differ-ent approach. We have been using multi-omics data integration to get new insights about key molecules involved in the tumor de-velopment. I will elaborate one such approach employed in our effort.

Dr. Amol SuryawanshiDesignation: Scientist-DInstitute: ILS, Bhubaneswar Email: [email protected]

Biography: Dr. Suryawanshi is an eminent sci-entist working in the field of clinical proteom-ics and Proteoinformatics in the Institute of Life Sciences, Bhubaneshwar. He is member of Human Proteome Organization (HUPO) since

2006. He is a Life member and presently Executive council mem-ber of Proteomics society of India (PSI) where his main interest is to carry educational activities towards popularization of proteom-ics. He is also life member of Laboratory Animals Scientist Asso-ciation, India (LASA), Society of Biological Chemists, India (SBC) and Indian Society for Mass Spectrometry (ISMAS). His major re-search focus includes Disease Proteome Mapping, Bio-marker dis-covery in various clinical diseases to decipher the role of important protein/s in disease pathogenesis and Identification and character-ization of post-transnational modifications (PTMs) with respect to their role in disease pathogenesis. He has extramural project grants including Young investigator grant. His research findings have been published in various reputed peer reviewed journals. He regularly organizes symposium and workshops on different areas of proteomics such as quantitative proteomics. He has suc-cessfully organised, “International Conference on Proteomics in Health and Disease along with 9th Annual Meeting of Proteomics Society, India (PSI)” during November 30-Dec 02, 2017 at Institute of Life Sciences (ILS), Bhubaneswar, Odisha.

Talk title: Proteomics approach leads to identify differentially expressed proteins involved in nasopharyngeal carcinoma

Abstract: Mass spectrometry based advanced proteomics ap-proaches have become promising for identification and quantifica-tion of differentially expressed proteins in high-throughput man-ner and further checks their ability to use as potential biomarker in clinical studies including cancer. Therefore, proteomics studies are very much important to understand the biology and disease patho-genesis. The broad goal of my lab is to discover the differentially expressed proteins involved during disease pathogenesis using ad-vanced Proteomics approaches and decipher their role to improve disease diagnosis, prognosis, therapies and prevention. Presently, we are working on various diseases including nasopharyngeal car-cinomaNasopharyngeal carcinoma (NPC) is a rare form of malignancy having remarkable geographic and racial distribution. Worldwide


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prevalence of NPC is mostly in East and Southeast Asia. In India, NPC is also rare except North eastern states and reported preva-lence rate of NPC is 1.82% amongst all cancers in this region. In this study, we aim to identify and validate the differentially ex-pressed protein from plasma sample of NPC cases and Controls from north eastern states of India using different proteomics ap-proaches such as 2D electrophoresis, iTRAQ etc. This talk will more elaborate on how we could use this approaches and identify differentially expressed protein probably involved in NPC patho-genesis. These proteins might be useful as diagnosis tool or disease progression marker, however further studies are needed.

Mr. Shailendra RaneDesignation: Assistant Manager Institute: Shimadzu (India) Pvt. Ltd.Email: [email protected]

Biography: Mr. Shailendra is M.Sc. in Bio-Ana-lytical chemistry from Mumbai University and currently working with Shimadzu (India) Pvt.

Ltd. as Assistant Manager since 2008, pursuing higher studies and submitted his thesis for Ph.D. degree titled as natural colorants ex-tracted from plants of Indian origin and their characterization by advanced hyphenated analytical techniques. At Shimadzu, his role involves pre-andpost-sales application sup-port to pharma, food safety and bio-similar customers pertaining to trouble shooting, tech transfer, method development and vali-dation. To his credit he has 10publications in various international journals of repute and around 30 posters he published in national and international conferences. His expertise lies in analysis of drug substances and products, various food matrices and bio-molecules with cutting edge technology like LCMS/LCMSMS from Shimad-zu with hands on experience on critical sample preparation steps involved. He delivers lectures on liquid chromatography and mass spectrometry at various national conferences. Also, he has been very actively involved in the performance evaluation of various chromatographic and advanced technologiesavailable with Shi-madzu like SFC, MALDI-TOF etc.

Talk title: Role of Micro-LC in proteomics

Abstract: Microflow liquid chromatography–tandem mass spec-trometry (LC–MS-MS) has seen a surge of attention, development, and popularity among research scientists and bioanalysts over the last few years. The NexeraMikros is a newly developed Micro-LC system from Shimadzu. It can be used to detect target components with higher sensitivity than with semi-micro flowrate compatible LCMS systems, which perform measurements within a flowrate range of 1µL/min to 500 µL/min. In addition, it features shorter analysis times and is more durable than nano flowrate compatible LCMS systems, which perform measurements within a flowrate range of several 100 nL/min to 1 µL/min. Furthermore, the NexeraMikros improves operability, and at the same time, enables high-sensitivity analysis with smaller system capacity. This is due to the UF-Link, which enables one-touch con-nection and disconnection between the LCMS ionization interface and the analytical columns. The potential of this technology to pro-vide better sensitivity, less solvent waste, near-zero dead volume,

and high throughput are a big part of this renewed interest in pro-teomics field.

Mr. Brendan MacLeanBiography: Refer to Targeted Proteomics section Talk title: Introduction to targeted proteom-ics & Skyline

Dr.Cristina ChivaBiography: Refer to Targeted Proteomics section Talk title: QCloud: A cloud-based quality control system for the proteomics commu-nity

Dr. Eva Borràs Biography: Refer to Targeted Proteomics section Talk title: Targeted proteomics in clinical re-search

Dr. Nathalie Selevsek Biography: Refer to Targeted Proteomics sec-tion Talk title: Investigation of post-translational modifications with PRM

Ms. Subhra PriyadarshiniDesignation: Chief Editor,Organization: Nature India, NPG groupEmail: [email protected]: Ms. Priyadarshini is the editor of Nature India, NPG group. She has a bache-lor’s degree in Zoology. She pursued law af-ter majoring in Personnel Management and Industrial Relations from Utkal University, Bhubaneswar, India and a post graduate from

the Indian Institute of Mass Communication, she also studied print journalism at the University of Westminster, London. She was a correspondent with major Indian dailies The Times of India, The Indian Express, The Asian Age, The Telegraph, news agency Press Trust of India and Down To Earth magazine. Nature India is her first online venture, which covers thorough in-depth features and commentaries by leading members of the scientific community.


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Talk title: Tell me a science story.Abstract: Why is it important for scientists to communicate their science to the public? What are the perceived risks and benefits of taking science out of the lab to the masses? In the age of social media and blogging, which are the best modes, beyond publishing in peer reviewed journals, to reach science and its many implica-tions to people? As India is poised to become a major player among the world’s leading science-faring nations, it is essential that her scientists brace up to become good communicators of their sci-ence. More often than not, our scientists are happy working in their labs and sharing their work and results with a limited number of peers. It is time the country’s scientists proactively participated in the process of informing the public about science, raising aware-ness of their scientific disciplines and inspiring a next generation of researchers. Apart from the whys and hows of communicating science, this talk will veer around what makes science interesting for people and for the media, understanding journalists and editors who cover sci-ence issues, and a primer on the most effective ways to use social media for science communication.


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CULTURAL EVENING


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The cultural evening program, the last session of International symposium, will witness the enchanting performances by many artists. The session will start with the stimulating talk by Ms. Subhra Priyadarshini followed by a Ganesh Vandana performance by Talele sisters; Shwetal and Ritvee.

The next performance will be by Master Suleiman, who also happens to be the winner of the reality-talent show, ’India’s Got Talent’ in the year 2016. With just a flute, a 13-year-old boy from Amritsar had both Bollywood and the national audience following his tune. Suleiman emerged as the winner on the seventh edition of India Got Talent and conquered the hearts of many, all thanks to his flute. Music and sense of tunes are something that he has inherited from his extremely talented parents, who too are professional musicians.The evening will also witness a folk dance performance by Dr. Tushar Guha who is an exponent in Indian Clas-sical Dance, Indian Folk Dance and Western Dance and has performed in more than 3500 shows all over the world. At 15 years of age, his passion for personality development and positive communication became obvious with his initiation of Nrityanjali –The Institute of Performing Arts, Education, Personality Development and Management Services.

He has got trained in the basics of Indian Classical Dances of Kathakali, Bharatanatyam, Manipuri, Kathak at Bharatiya Nritya Kala Mandir while simultaneously pursuing dramatics and music. Pursuing Kathak under doyen Lachhu Maharaj and conducting in-depth research on folk dances of rural India for 30 years, he successfully communicates the wealth of Indian folk dances of multiple states to the urban audience through his dance performances. The dances represent various states of India – Kerala, Tamil Nadu, Maharashtra, West Ben-gal, Goa, Assam, Mizoram, to mention a few. He has received the rare privilege of choreographing and directing the 50th year of Geet Ramayan with 150 artistes. Under his able guidance, Nrityanjali has performed for various prestigious occasions including Kullu Dassera Festival, Kalaghoda Arts Festival, NCPA-Tata Theatre and Experi-mental Theatre, India India Festival Switzerland, ITB Festival Germany, Italy.

Ms.


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Satellite symposium IIT Goa


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Preamble to the Satellite Symposium IIT Goa

The Proteomics symposium at IIT Goa is one of the first initiatives to bring in international experts in the field of Proteomics to inspire innovative thinking in young students. This event was recently held at IIT Goa on 22nd February, 2018 at the GEC auditorium. This is a half day symposium which featured five lectures by the leading scientists in the field. The lectures were designed to cover a wide spectrum of topics in this area ranging from Introduction to Proteomics and Targeted proteomics to its various applications in the field of quality control and clinical biomarker research. The symposium aims to attract early career researchers as well as experienced scientists and gives them an excellent opportunity to explore the state-of-the-art technologies in the field of proteomics research.

Although this conference focused on ‘Targeted Proteomics’ but we have tried to provide the glimpse of various disciplines of proteomics to give a broad overview of proteomics field. This symposium also provided an excellent opportunity for students to interact with international experts in this area to develop an understanding of science and technology that goes way beyond textbooks and classrooms. It is noteworthy that the plenary speaker Mr. Brendan MacLean who has made significant contributions to the field of Proteomics is a software engineer by profession and not a biologist. Scientific discussions with Mr. Brendan MacLean motivated IIT Goa engineering undergrad students to integrate their engineering principles and knowledge in the field of biology to develop relevant technological solutions.

Prof. Sanjeeva Srivastava, IIT Bombay commenced the symposium with a lecture on the basics of Proteomics. This was followed by a talk on ‘Targeted Proteomics and skyline’ by plenary speaker Mr. Brendan MacLean, University of Washington, USA. Invited talks were delivered by Drs. Cristina and Eva Borràs, Proteomics Unit Barcelona and Dr. Nathalie Selevsek from ETH Zurich, Switzerland on Q-cloud, targeted proteomics in clinical research and investigations of post-translational modifications with PRM, respectively.

Satellite Symposium IIT Goa schedule(Thursday, 22nd feb, 2018)

Time ACTIVITY08:30 - 09:00 AM Registration09:00 - 09:15AM Invocation and welcome address09:15 - 10:15 AM Lecture: Dr. Sanjeeva Srivastava – An Introduction to

Proteomics10:15 -11:00 AM Plenary talk: Mr. Brendan MacLean – Introduction to

targeted proteomics & Skyline11:00 - 11:30 AM Tea Break11:30 - 12:00 PM Invited talk: Dr. Cristina Chiva – A cloud-based quali-

ty control system for the proteomics community12:00 - 12:30 PM Invited talk: Dr. Eva Borràs – Targeted Proteomics in

Clinical Research12:30 - 01:00 PM Invited talk: Dr. Nathalie Selevsek – Investigation of

posttranslational modifications with PRM01:00 -01:10 PM Concluding remarks


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General information


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Proteomics milestones


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Preamble to the Proteomics Milestones

The Human Genome Project has brought us closer to a holistic understanding of human physiology; however, the complexity of biological systems has necessitated the emergence of allied –omics based approaches. The 21st century, deemed as the

age of revolution in bioscience research, has witnessed the emergence of “proteomics”, a field where scientists aim to understand the composition and interplay of the proteins in biological systems. The findings and consequence of such proteomics based research has helped to enhance systemic understanding of biology and has also found immense translational potential. Ever since its inception, proteomic based platforms have seen an exponential growth due to the rise in sophistication of technologies that can be attributed to few key milestones. This section aims to overview the path that has led to the establishment of Proteomics, as we know it today. A journey of proteomic technologies since its inception, various milestones and present day modalities have been discussed here.

The journey of “Proteomics”, from its inception to present day modalities can be attributed to the advancements in engineering, power of bioinformatics to handle the high-throughput data and zest among researchers to push the boundaries of conventional global proteomics profiles. The findings and consequences of such proteomics based research have helped in the systemic understanding of biology, which has found immense applications in translational research. With proteomics at its leading edge, organization like the HUPO have provided a common platform in the form of collaborative mega-projects, thus bringing the global proteomics expertise together for the completion of the human proteome project.

In this section, we review the success stories of proteomics platforms such as two-dimensional electrophoresis, mass spectrometry, protein microarray technology. This also highlights the contributions of global bodies like Proteomics Society of India (PSI) & Human Proteome Organization (HUPO), and efforts that are leading towards the completion of the human proteome project.


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While the human genome project has revealed a total of ~20,000 genes, the number of proteins continues to remain high owing to several mechanisms like alternative splicing. Proteins, one of the most complex macro-molecules, have intricacies at several levels, namely; different amino acid side chain groups, secondary structure elements, tertiary structure interactions etc. that are furthermore confounded by the post-translational modifica-tions.


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Genomics and proteomics, the two complementary fields of modern science, are often studied together to answer some of the challenging biological questions. Although genomics pursue to unravel the genetic code, proteomics, on the other hand, explores the structural and functional aspects of proteins, which are eventually the effector molecules in a biological system


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Proteomics, a relatively newer field in comparison to its more traditional counterparts like genomics and tran-scriptomics has garnered a lot of accolades in the last decade and has revolutionized research by the application of high-throughput techniques such as two-dimensional gel electrophoresis, mass spectrometry and protein arrays.


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1. Gel based Proteomics

Gel-based proteomics studies, fundamentally, involves the separation, detection, estimation and identification of proteins, so as to find new avenues in quantitative studies and novel molecular targets in biomarker research. Electrophoresis, a gel-based method to separate proteins, was invented by Prof. Tiselius in 1930. Later, Laemmli developed the SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) involving proteins denatured using sodium dodecyl sulfate (SDS), followed by separation through an acrylamide-bisacrylamide polymer matrix by applying an electrical gradient. These SDS bound proteins have a net negative charge, thus, they differentially migrate in the gel primarily based on molecular weight. While one dimension gel electrophoresis relies on molecular weight based separation of proteins, it has limited resolution.

The innovative idea of separating proteins in two dimensions based on isoelectric pH and molecular weight of proteins led to the discovery of two dimensional gel electrophoresis (2-DE). Klose (native IEF and SDS-PAGE) and O’Farrell (denaturing IEF and SDS-PAGE) had discovered the 2-DE technology in 1975 inde-pendently by coupling isoelectric focusing (IEF) with SDS-PAGE. Initially, the use of glass tube-based isoelectric focusing (IEF) was predominant; however, this presented many challenges in reproducibility, ease of use and throughput. Bjellqvist and Righetti used immobilized pH gradient strips for isoelectric focusing and Angelika Gorg developed a method to use IPG strips in 2-DE using a thin acrylamide gel slab mixed with pH gradients backed by a plastic film in 1982 which took 2-DE to the next level. 2-DE has been effectively used to study differ-ential proteomic analysis, isoform separation, and analysis of post-translational modifications. The emergence of fluorescent dyes has significantly contributed to the arsenal of applications in gel-based proteomics by increasing its reproducibility and sensitivity.

Activity-based protein profiling using gel-based proteomics through the introduction of enzyme-target-ing probes allowed the researchers to get information regarding protein activity apart from relative abundance. Cyanine dyes with Cy2, Cy3 and Cy5 variants have significantly helped in development of techniques like differ-ential-in-gel electrophoresis (2D-DIGE), which has made gel-based platforms robust platforms for quantitative proteomic studies.

• TwoDimensional-GelElectrophoresis(2-DE)

Gel-based proteomics is one of the versatile fields of proteomics, which has provided us with tools that can be used for protein separation, characterization as well as quantification. The goal of proteomic studies is to detect altered protein expression and modifications associated with disease or to find molecular targets for biomarkers and therapy.

Gel-based proteomics includes techniques like one-dimensional SDS-PAGE or Native PAGE, 2-DE and 2D-DIGE. The proteins that are differentially expressed can be further identified using techniques like Mass Spec-trometry. Gel-based proteomics mainly exploits the principle of electrophoresis and provides information about protein properties such as molecular weight and isoelectric point. Gel-based proteomics includes techniques like one-dimensional SDS-PAGE or Native PAGE, 2-DE and 2D-DIGE. The proteins that are differentially expressed can be further identified using techniques like Mass Spectrometry. Gel-based proteomics mainly exploits the prin-ciple of electrophoresis and provides information about protein properties such as molecular weight and isoelec-tric point.

Principle: Two-dimensional gel electrophoresis (2-D electrophoresis) is a widely used technique for the analysis of complex protein mixtures. This method separate proteins in two steps, the first-dimension is isoelectric focusing, which separates proteins according to their isoelectric point; the second-dimension is SDS-polyacryl-


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amide gel electrophoresis (SDS-PAGE), which separates proteins according to their molecular weight. In this way, complex mixtures consisting of thousands of different proteins can be separated. Two types of reagents are used in 2-DE buffers to ensure protein solubility and denaturation. The first type, chaotropes (e.g. urea, thiourea and CHAPS), used at multimolar concentrations, is able to unfold proteins by weakening non-covalent bonds (hydro-phobic interactions, hydrogen bonds) between proteins. The second one is ionic detergents, in which SDS (sodium dodecyl sulfate) is the archetype. It is made of a long and flexible hydrocarbon chain linked to an ionic polar head. The detergent molecules will bind through their hydrophobic hydrocarbon tail to hydrophobic amino acids. This binding favors amino acid-detergent interactions over amino acid-amino acid interactions, thereby promoting denaturation. Moreover, nonionic or zwitterionic detergents such as Triton X-100 are also used for protein sol-ubilisation, since IEF requires low ion concentration in the sample. The detection method post-gel migration is achieved either by the use of visible stains such as silver and Coomassie or fluorescent stains such as Sypro Ruby.

2-DE Workflow: It involves the following steps: Rehydration of IPG strip, Isoelectric focusing of Rehydrated IPG strip (1st dimen-sion), 2nd dimensional SDS-PAGE, Staining and destaining and Image analysis using IMP7 software.

• Two Dimensional- Difference In Gel Electrophoresis (2D-DIGE)

Principle: Two Dimensional-Differential Gel electrophoresis (2D-DIGE) is an advancement over conventional two dimensional gel electrophoresis (2-DE) and involves the use of fluorescent dyes called CyDyes for labeling protein samples. This technique has greatly helped in improving the sensitivity, accuracy and reproducibility of 2-DE in terms of quantitation. CyDyes are fluorescent labels with similar mass and charge, pH insensitive and photostable with each label emitting a distinct, highly sensitive signal. Minimal labeling of the samples using Cy-Dyes ensures that each visualized protein has a single dye molecule effectively labeling only 3% of the total protein in each sample. During labeling, the NHS-ester reactive group of CyDyes binds to the ε amino group of Lysine resulting in addition of mass by 500 Daltons and replacement of the positive charge on Lysine with the positive charge of the CyDye thereby maintaining the pI of the protein.The labeling of samples using CyDyes in 2D-DIGE allows comparison of samples from two different conditions across large datasets, not possible using 2-DE due to gel-to-gel variation. Also, the reduced number of gels required for comparison of proteomes using 2D-DIGE saves a lot of time and energy thereby making analysis very easy.

Workflow of 2D-DIGE: It involves the same steps as that of 2-DE except that here samples are first labelled and then the procedure is followed. After the samples are labelled same procedure is followed i.e. 1. Protein labelling with CyDyes2. Rehydration and Isoelectric focusing (first dimension)

Overall workflow of 2-DE (Two dimensional gel electrophoresis)


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3. Equilibration of IPG strips4. SDS-PAGE (second dimension)5. Staining – gel visualization6. Image analysis7. Spot picking8. Enzymatic digestion & MS analysis

REHYDRATION OF IPG STRIP

Strategy of sample labelling with Cydyes for 2D-DIGE

B. SDS-PAGE (2nd Dimension) A. Isoelectric focussing of IPG strips


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Both the groups found evidence for many proteins that had not been previously analysed, using mass spectrom-etry and genome annotation. Pandey and colleagues detected about 84% of the 20,000 human protein-coding genes. Pandey’s lab studied 30 normal tissues, i.e., adult tissue, primary hematopoietic cells and fetal tissues and subjected them to comprehensive, label-free quantitative mass spectrometry analysis. Kuster’s team profiled 60 tissues, 13 body fluids and 147 cell lines.

2.Mass spectrometry in Proteomics

Mass spectrometry, a powerful tool to identify a molecule on the basis of mass to charge (m/z) ratio, was pioneered by Sir J.J. Thompson about a century ago [17]. This invaluable technique has evolved significantly over-time and now penetrates a multitude of scientific disciplines, including proteomics.

The development of soft ionization techniques, such as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI), were crucial breakthroughs in mass spectrometry, allowing it’s use for identification of biological macromolecules such as proteins. Soft ionization techniques enabled the production of ions with controlled fragment-ion content, which was of essence, considering the labile nature of proteins. The ESI mass spectrometer generates ions by spraying a dilute solution of analyte (peptide/protein) molecules through a fine metal capillary tip (taylor cone), which leads to the formation of very fine droplets. The droplets, when subjected to an electrical field, become highly charged, and as the solvent evaporates, the peptide molecules in droplet get ionized by proton exchange. Although Malcolm Dole from Northwestern University was the first to use electron spray ionization with mass spectrometry in 1968, it was John B. Fenn at Yale University who truly developed ESI in the late 1980s, for which he received the 2002 Nobel Prize in Chemistry.


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Both the groups found evidence for many proteins that had not been previously analysed, using mass spectrom-etry and genome annotation. Pandey and colleagues detected about 84% of the 20,000 human protein-coding genes. Pandey’s lab studied 30 normal tissues, i.e., adult tissue, primary hematopoietic cells and fetal tissues and subjected them to comprehensive, label-free quantitative mass spectrometry analysis. Kuster’s team profiled 60 tissues, 13 body fluids and 147 cell lines.

2.Mass spectrometry in Proteomics

Mass spectrometry, a powerful tool to identify a molecule on the basis of mass to charge (m/z) ratio, was pioneered by Sir J.J. Thompson about a century ago [17]. This invaluable technique has evolved significantly over-time and now penetrates a multitude of scientific disciplines, including proteomics.


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• Bottom–upApproachofMassspectrometryAlthough techniques such as 2-DE and 2D-DIGE could achieve protein separation from complex biospecimens, there is need to identify proteins present biologically in


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low abundance. This demand of enhanced detection sensitivity along with high reproducibility led to the emer-gence of shotgun proteomics. The term “shotgun proteomics” was coined in 1998 and was analogous to the idea of “shotgun sequencing” used in DNA sequencing. Just like the latter, shotgun proteomics allowed high-through-put identification and quantification of proteins, where multiple proteins could be analyzed from complex mix-tures in a single run, in a timely and sensitive manner. This enabled researchers to identify many low abundance proteins, which were otherwise missed in traditional gel-based techniques. Shotgun proteomics is a bottom-up approach, where enzymatically fragmented protein mixtures could be identified using tandem MS. In this


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technique, proteins from complex mixtures are broken down using enzymes to generate smaller fragment pep-tides. The peptides thus generated, could be used as surrogate representatives of their original sample amount. The proteins are fractionized using strong cation exchange (SCX) chromatography or multidimensional protein identification technology (MudPIT. Ionized precursor fragments are selected in the first stage of MS and the fragmented ions are subsequently analyzed in the second stage of MS. The spectral data generated is compared with existing protein sequence and decoy databases, which provides probability of protein identification with high confidence.

• Top-downapproachinMassSpectrometrybasedProteomics“Top-down” approach is another mass spectrometry based method used for identification of proteins with improved sequence coverage. It allows one to identify PTM modifications on the protein. Top-down proteomics method uses advanced fragmentation methods such ECD or ETD to detect PTM modifications, however they cannot be used for high-throughput analysis.

• TargetedProteomics:Targeted proteomics has emerged as an alternative to circumvent the hurdles poised by shotgun proteomics, which has now enabled the identification and quantification of a protein or panel of proteins in biological sam-ples. This approach was explored in the 1960s using antibodies against a protein of interest, however generation of highly specific antibodies was one of the major challenges in this approach. Kondrat, McClusky and Cooks introduced the technique called, Selected Reaction Monitoring (SRM) to quantify a protein of interest in bio-logical samples. “Targeted proteomics”, was re-explored by Aebersold group to accurately quantify a protein of interest or a subset of proteins from complex biological specimen by improving specificity and sensitivity using high performance mass spectrometry.


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• QuantitativeProteomicsGel-based proteomics such as 2-DE and DIGE have been used for quantitation of the proteins however, techni-cal hurdles such as low reproducibility, coverage, sensitivity and throughput led to the development of alternate modalities for protein quantitation. Mass spectrometry based platforms have enabled quantitation of thousands of protein in a single run. Gygi SP and Aebersold R were the forerunners of isotope coded affinity tags (ICAT) technology in combination with tandem mass spectrometry which enabled effective protein identification and accurate quantification. Later, Mann M and Pandey A had developed an in vivo labelling technique for mammali-an proteins using isotopic amino acid and the method termed as Stable Isotope Labelling by Amino acids in Cell culture (SILAC), which is very popular for labelling and quantitation of proteins in cell culture or bacterial culture. Pappin DJ introduced isobaric tags for relative and absolute quantification (iTRAQ), for tagging digested peptides, allowing quantification of peptides/proteins based on the intensity of the iTRAQ reporter ion. Similarly, Hamon C developed tandem mass tags (TMT) for labelling the digested peptides and quantified the peptides/proteins based on MS/MS fragmentation spectra. TMT and iTRAQ methods have advanced progressively over the period of time and are now available as Eight-plex systems in iTRAQ and Ten-plex kits in case of TMT. The major advantage of mass spectrometry based quantitation is multiplexing, high sensitivity, dynamic range and accurate quantification. Emergence of such quantitative based proteomics has been a key milestone and game-changer in this discipline.


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After the completion of the Human Genome Project, high-throughput technologies like DNA microarrays came into play which provided the functional analysis and profiling of gene expression in whole cell, tissues and or-ganism.


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3. Proteins Microarray technology

Protein microarrays are mainly used to study high-throughput protein-ligand interactions to understand complex biological pathways. This ligand could be a protein, DNA, RNA or a synthetic compound. Following the successful completion of the Human Genome Project, high-throughput technologies such as DNA microarrays have enabled the detailed analysis and profiling of gene expression in whole organisms, cells and tissues. DNA microarrays pre-sented limitations like poor correlation between gene expression and its respective protein expression levels, which drive the phenotype of an organism. Post-translational modifications also presented a unique challenge in terms of functional alterations, which cannot be completely understood through DNA based platforms. The success of DNA-based array platforms inspired the development of protein microarrays, to follow the path of DNA arrays, so as to replicate its success at a different level.

Protein microarrays are grids, which contain small amounts of purified proteins in a high density. Zhu and Snyder developed protein arrays comprising of 6000 purified yeast proteins, which was one of the first practical platforms for utilizing protein arrays for sustainable interactomics based studies. Zhu and co-workers went on to further develop high-density protein arrays comprising of as many as 17000 recombinant human proteins printed on the first version on the Human Proteome Arrays (HuProtTM). This platform has now been further developed to the HuProtTM v2 containing around 19000 recombinant human proteins from Cambridge Protein Arrays. Cell-free based protein microarrays such as nucleic acid programmable protein microarray (NAPPA), DNA array to protein array (DAPA) and Protein in Situ Array (PISA) have emerged to overcome the issues in protein purifi-cation and storage. HaloTagTM protein is an engineered bacterial enzyme based protein tag which can be fused to any given protein of interest. The halo-tagged protein is capable of covalently and irreversibly binding to its ligand. This interaction is very specific and the tagged proteins can be further sub-tagged, enabling a multitude of applications such as protein capture and protein imaging.

The last few decades have seen tremendous innovation in label free technologies such as SPR (Surface Plas-mon Resonance), BLI (Bio Layer Interferometry, microcantilever, carbon nano-tubes and nano-wires and so on. Few of these technologies have reached practical applications; however, many of them presently remain as “proof of concept” technologies.


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Human Protein Atlas, initiated in 2003, was conceptualized with the objective of mapping all the human proteins in cells, tissues and organs by employing various approaches like antibody-based imaging, mass spectrometry and systems biology.


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ABOUTHUMANPROTEOMEORGANIZATION(HUPO)

Over the last four decades, proteomics technologies have evolved tremendously and have provided the best possible platforms to the end user. Applications of these technologies have evolved progressively in all bio-logical disciplines right from studying unicellular microbes to studying the complex human system. After

deciphering the human genome sequence, the scientific community took a decade to complete the human pro-teome map. Mass spectrometry and protein microarrays have been at the frontier of realizing this goal. To this end, Human Proteome Organization (HUPO) has provided an umbrella for the proteomics community. Since its estab-lishment, the HUPO has initiated several mega-projects. Among them, Chromosome Centric Human Proteome Project (C-HPP) and Biology/Disease driven Human Proteome Project (B/D-HPP) are two major initiatives to complete the human proteome map. Alongside, Pandey (Johns Hopkins University, USA), Kuster (TUM School of Life Sciences, Germany), and Uhlen (KTH- Royal Institute of Technology, Sweden) groups have provided the first human proteome drafts independently using high-resolution mass spectrometry or antibody based microarray.

With these collective efforts, ~90% of human proteome coverage was achieved, however the completion of the human proteome map is a goal, yet to be realized. Heck has strongly emphasized that analyzing samples with multi-protease digestion can help in identifying many missing proteins, large-scale protein interactions in human proteins and dynamic phosphorylation of proteins. Besides, many databases such as neXtProt. PeptideAatlas, the Human Proteome Atlas, proteomeDB, human proteome map etc. have evolved to support the human proteome project by curating data from the literature. Projects like the C-HPP also complement the Human Proteome Proj-ect (HPP) towards its completion. Human genome sequencing is now possible in a mere span of few hours and personalized genomic libraries currently exist for many individuals.

Future goals are directed towards having proteo-genomic profiling available as a modality for humans to realize personalized medicine as an integral part of diagnosis and treatment regimes.

Human Proteome Project (HPP) aims at characterization of all 20,000 genes of human genome. The Project will generate a proteome map of the human body which can become a resource to help understand the biological and molecular function and may aid in treatment of diseases.


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Proteogenomics can be used to provide information about the effects of genetic variations on the final products of gene expression hence providing a better understanding of genotype- phenotype inter-relationship.


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ABOUTPROTEOMICSSOCIETYOFINDIA(PSI)

In early 2002, after a slumber of near three decades, Protein and Proteomics Research reemerged as a Science requiring attention. This received impetus after the completion of the human genome sequence in April 2003. Since then, there are worldwide efforts to develop technologies for purification, identification, charac-

terization, quantification, functional annotation of proteins, global protein profiling and generating a hu-man proteome map. These include developments for mass spectrometry, bioinformatics and antibodies, which are now considered the three pillars of Proteomics.

In India too, the scientific community used global protein profiling for biological investigations since the late 1970s. In 2009, several senior scientists felt the need to bring together the upcoming Pro-teomics community in India. The Proteomics Society, India (PSI) was registered in 2009 to provide the required forum. The Society emerged from the initiatives of Dr. Ravi Sirdeshmukh, Dr. M.A. Vijayalakshmi, Dr. Shantanu Sengupta and several others. As the research efforts expand and technologies evolve, it is important to facilitate interactions among the Proteomics community and help them share knowledge for the growth of this field. “Proteomics Society, India”, is thus formed to provide a forum to pursue an agenda that will meet this objective.

The Proteomics Society, India (PSI) has a mandate to promote and advance proteomics research through meetings and workshops to provide state of the art information to the proteomics community. Individual Sci-entists in laboratories equipped with the required instrumentation have provided the necessary expertise to colleagues across India in addressing their biological queries requiring proteomic tools. Proteomics has now emerged as an important tool for varied biological investigations in the country. Proteomics for Toxicolo-gy and Chemoprevention are the focus of investigations in the laboratories in Lucknow.

The IIT Bombay team has initiated the virtual proteomics forum for promoting proteomics through the internet. The multi- institutional efforts of the Institute of Bioinformatics group in Bengaluru have provided the first draft of the human proteome. In parallel with proteomics, metabolomics is receiving immense attention in several laboratories. It is apparent that the Society is acting as a node for international collaborations as well as an important forum for updating proteomics among the student and teacher community.


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Outreach efforts: Proteomics Documentaries


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Proteomics - Translating the Code of Life

The completion of Human Genome Project was a major landmark achievement for the life sciences community. With genomics setting a foundation in the quest to un-cover the mysteries of life and biology, what lies next? What are the prospects and challenges as we explore the post-genomic world? Proteins and proteomics are central to connecting genomes with phenotypes and biological function. Proteomics provides a veritable foundation to address whole systems and uses a broad unbiased approach to decipher post-genomic biology. This documentary portrays the journey of “Proteom-ics”, discusses its advancements, achievements and key issues that lay ahead. The first section of the documen-tary introduces the post-genomic era and establishes the necessity of proteomics. The second section focuses on the development of various proteomic technologi-cal platforms and how persistent efforts of proteomics scientists have resulted in the First Draft of the Human Proteome. Next Generation Tools involving Trans-Pro-teomic Pipeline, SWATH-MS and Skyline have added to the arsenal of targeted proteomics. The proteomics community can contribute immensely to functional biology and offer innovative solutions in life sciences. Sustained and committed efforts from global proteomics communities like the Human Proteome Organization (HUPO) have helped proteomics establish an undeniable international presence. This has helped define the broad-er theme of research directions, thus, “Translating the Code of Life”.

Human Proteome Project

The Human Proteome Project (HPP), a HUPO ini-tiative aims at identifying and characterizing each of the human proteins predicted after analysis of the hu-man genome, through concerted efforts of scientists and laboratories around the world. The HPP has two major goals: (1) Completion of protein parts list in a step-wise manner and (2) Making proteomics an important component of biomedical and life science community alongside genomics. In order to achieve the set goals, the HPP initiatives have been broadly categorized into the Chromosome Centric Human Proteome Project (C-HPP), Biology/ Disease Human Proteome Project (B/D-HPP) and Resource Pillars Human Proteome Project. The C-HPP focuses on un-derstanding the human proteome at the chromosome level, while the B/D HPP aims at proteome level alter-ations accompanying the biology of different diseases. The Resource pillars human proteome project include the


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use of Antibodies, Mass spectrometry and bioinformatics tools like neXtProt and TPP to increase the confidence of the data for comparison, exchange and verification based on guidelines laid down by the Proteomics Standard Initiative (PSI). Completion of the Human proteome project will enhance understanding of human biology at the cellular level and lay a foundation for the development of diagnostic, prognostic, therapeutic and preventive medical applications. The HUPO Congress has included a number of educational and promotional activities that together we hope will raise awareness of the achievements of proteomics and also support the training of young scientists wishing to pursue a career in the field. This documentary on “Human Proteome Project (HPP)” produced by IIT Bombay team highlights the journey of HPP, its progress, achievements and key issues that lay ahead. India Beckons

India Beckons portrays the story of a scientist trained at Harvard University, seeking to contribute to world class clinical proteomics research in his motherland India. The protagonist overviews his journey and hurdles faced by him to fulfill his goal of setting up a world-class proteomics research facility in India. With a vision for innovation, Indian Institute of Technology Bom-bay, a premier institute in India, provided the protagonist with a platform and the basic facilities to set up a lab. “India Beckons” is about hard-work, perseverance and the vision for a better tomorrow, which can transform difficulties into opportunities and dreams into realities. It is not just about the physical journey that an individual takes but the metaphoric journey which inspires one to come back and pay homage to their motherland by contributing to its develop-ment.


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ABOUTINDIANINSTITUTEOFTECHNOLOGYBOMBAY

Indian Institute of Technology (IIT) Bombay is known to be one of the premier institutes for the higher educa-tion and research in India. Over the years IIT Bombay has extended its abilities to contribute to quality teach-ing and research in almost all fields of science and technology through state-of-the-art facilities for academia

and researchers. The Department of Biosciences and Bioengineering at IIT Bombay has put in balanced endeav-ours to be a part of basic science and applications in the field of biology, bio-medical and bioengineering research.Proteomics is an emerging field of re-search globally and IIT Bombay aims to keep-up the pace in this burgeon-ing field, which aims to identify pro-teins that are characteristic for disease formation & progression, and can po-tentially uncover diagnostic, prognos-tic markers or novel drug targets, and could help to understand the underlying mechanisms. IIT Bombay is emerging as a vibrant hub of bio-research and proteomics in India. At IIT Bombay currently research on proteomics and protein biochemistry is being pur-sued at various levels, e.g. Disease proteomics of glioblastoma, meningioma, malaria pathobiology, proteomics involving cell division of prokaryotic & eukaryotic cells, and recombinant proteins and protein structure analysis by developing and applying high end bioinformatics and statistical techniques.

To ensure high quality research, IIT has set its benchmark on par with some of the best institutes nationally and internationally. During the last two years IIT Bombay has set-up several high throughput platforms for the proteomics analysis such as GenePix4000B Microarray Scanner for Protein Microarray studies, OmniGrid Accent Microarrayer for printing of microarray slides, Autoflex MALDI TOF/TOF for mass spectrometry, 6550 iFunnel Q-TOF for mass spectrometry, Orbitrap for MS. Biacore T-200 for label free and protein interaction studies, Ty-phoon FLA 9500 scanner for 2D-DIGE experiments, Ettan IPG-phor 3 IEF System and Ettan DALTsix electropho-resis units for 2D gel based experiments. Other facilities like High Performance Liquid Chromatography (HPLC), Fast Performance Liquid Chromatography (FPLC) and Protein sequencer are also available. For analyzing the sizable data generated through these high throughput techniques, IIT Bombay also boasts a list of sophisticated software dedicated to each of the above techniques such as Spectrum Mill, Mass Profiler Professional, Acuity, De cyder 2D Differential Analysis software, ImageMaster Platinum, BIAevaluation, Proteome Discoverer and Mascot are few amongst them. Faculty expertise in the Department of Biosciences and Bioengineering,

IIT Bombay ranges from the basic Biological Sciences to Biochemical Engineering and Computer Sci-ences and Engineering. This breadth and depth is necessary to meet the demands of Systems Biology and Omics research. Researchers at IIT Bombay look forward to contribute actively to the field of science with few groups dedicated to proteomics and systems biology research.Together, with the Proteomics Society, India, we share the vision to be innovative and pioneer, and contribute to cutting edge proteomics research to set benchmarks at the international level by interactions, collaborations and continued perseverance.


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Sponsors/Partners


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DIAMOND SPONSORS

SHIMADZU SHIMADZU Analytical (I) Pvt Ltd is a wholly owned subsidiary of Shimadzu Corporation, Japan - one of the leading Manufacturers Suppliers of Analytical Scientific Instruments such as CHROMATOGRAPHY, MASS-SPECTROME-TRY, SPECTROSCOPY, PHYSICAL TESTING, LIFE SCIENCES, ENVIRON-MENTAL Monitoring instruments. We provide an extensive range of products value added services and customer support Shimadzu has been serving the In-dian customers since many years through its established network of distributors namely Toshvin Analytical, Spinco Biotech, Swan Environmental, Saksham Analytical & Amkette Analytics for various product ranges. SHIMADZU Analytical (I) Pvt Ltd reaffirms our continued commitment towards our valued customers. Our key strength has been continuously evolving new applications and providing solutions for challenging scientific queries. We have been relentlessly developing solutions for targeted proteomics, glycomics, mAb analysis giving a complete array of ready to use answers forscientific queries for protein determination and quantitation.URL: http://www.shimadzu.com/

THERMO FISHER SCIENTIFIC Thermo Fisher Scientific Inc. is the world leader in serving science, with revenues of more than $20 billion and approximately 65,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics, deliver medicines to market and increase laboratory productivity. Through our premier brands – Thermo Scientific, Applied Biosyste-ms, Invitrogen, Fisher Scientific and Unity Lab Services – we offer an unmatched combination of innovative tech-nologies, purchasing convenience and comprehensive servicesURL: http://www.thermoscientific.com/

GOLD SPONSORSAGILENT TECHNOLOGIESAgilent Technologies offers a comprehensive and complete portfolio of Proteomics products for every stepof the workflow, from sample prep through separation, detection and analysis. Agilent’s innovation & solutions set the standard for precision, generating highly reproducibleand reliable data for yourprotein analysis research. Agilent is the preferred part-ner for supporting every step of multi-omics integrated Biology projects, from data acquisition to data analysis and visualization. Moreover, Agilent is the only provider who can offer such a solution –we continue to lead the industry in the development and implementation of the tools and resources necessary to enable powerful analysis through integrated Biology. Analytical scientists and clinical researchers worldwide relyon Agilent to help fulfill their most complex laboratory demands. Our instruments, software, services and consumable address the full range of scientific and laboratory management needs so our customers can do what they do best: improve the world around us whether a laboratory is engaged in environmental testing, academic, research, medical diagnostics, pharmaceuticals, petrochemical or food test-ing. Agilent provides laboratory solutions tomeet their full spectrum of needs. We work closely with customers to help address global trends that impact human health and the environment, and to anticipate future scientific needs. Our solutions improve the efficiency of the entire laboratory, from sample prep to data interpretation and management.URL: http://www.agilent.com/


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PALL CORPORATION Pall Corporation has become a global leader in the high-tech filtration, separation, and purification industry by meeting the diverse needs of customers across the broad spectrumof life sciences and industry. The company’shighly-engineered process solutions protect people and critical assets, while minimizing emissions and waste. Our single-use systems enable faster,more efficient processes for our customers. Pall Life Sciences caters to the diverse and rapidly expanding biopharmaceuticals market. The products and technologies are used from the earliest stages of discovery and development of new drugs, through production and delivery of therapies for the prevention, diagnosis and treatment of disease. ForteBio is a wholly-owned subsidiary of Pall Corp. and a division of Pall Life Sciences.ForteBio developsanalyti-cal systems that enable real-time analysis of biomolecular interactions (protein quantification and characterization of protein-protein interactions, etc.) in micro-volume sample sizes, providinginformation on affinity, kinetics, and concentration.ForteBio utilizes proprietary Bio-Layer Interferometry (BLI) to create self-calibrating, simple-to-use, and inexpensive instruments that streamline measuring molecular interactions. An entire analysis can be completed in minutes and does not require labeling of the probe or the target. ForteBio’s analytical capabilities provide greater value in applications where existing methods (e.g., HPLC, ELISA, and surface plasmon resonance) have limitations in throughput, performance and cost. Pall Life Sciences brands now include ForteBio®, Octet®, BLItz®, Dipand Read™biosensors, and Sidekick™.URL: http://www.pall.com/

ARRAYJET- Innovative microarray solutionsArrayjet are leading providers of innovative microarray solutions to researchers, drug development groups and diagnostic companies world-wide. Founded in 2001, Arrayjet have vast mi-croarray expertise with a laboratory team having in excess of 75 years combined experience. With an installation base across 25 countries world-wide, Array-jet’s technology is well established and proven. Offering a flexible, customer fo-cussed approach with the provision of Arrayjet Advance™ microarray services, our in-house printing service, in addition to four scalable microarray instru-ments ranging from 100 slides to 1000 slide fully automated mass manufacturing capacity. Arrayjet also offer con-sumables, accessories and service support to maximise instrument performance. Arrayjet’s platform technology uses unique, non-contact, inkjet printing offering unrivalled speed, reproducibility and precision. It delivers high quality microarrays faster than any other technology with the ability to print any sample type onto a wide variety of substrates. With a proven and well established printing technology and vast microarray expertise Arrayjet are your ideal partner whatever your microarray needs. URL: www.arrayjet.com

PREMASPremas Life Sciences Pvt Ltd (PLS) is engaged in distribution of Industry-leading & game changing molecular technologies across India. Our products range from high end genomics equipments and associated services to reagents and consumables, thereby enabling researchers with analytical tools to address key molecular biology research questions. In a short span of time, we have created an enviable reputation of high-quality pre-sales and after-sales support to our customer base, via a dynamic network of motivated profes-sionals based across the key cities of India.Illumina is a Global Leader in the area of Genomics and Premas is representing Illumina as its Exclusive Sales Channel Partner in India. Jointly, we provide integrated solutions for multidisciplinary research across academic and industrial laboratories and the myriad applications that we cater to include:•LifeScienceResearch(BothgovernmentandPrivatelabs)•DrugDiscovery


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PARTNERS

SAI RAM EVENTSSai Ram Events, founded by Mr. Avinash Kanade, is full service marketing company providing on ground and online solutions. Sai Ram Events believes in delivering sim-ple, insightful and creative solution via digital marketing, events, experiential market-ing and corporate hospitality. With a wealth of knowledge and successful partnership their full service marketing division will help you solve your marketing challenges anywhere in India. Whether you want to boost, motivate, entertain or simply celebrate with your audience Sai ram Events team will help you create new and engaging solutions.URL: www.sairamevents.in

SPINCO BIOTECHSpinco Biotech’s team of 500 strong Spincoites form a network of 33 offices across the country celebrates 37 years of customer support. Spinco Biotech have streamlined their products from leading technology providers into strategic business units, name-ly Chromatography and Mass Spectrometry, Life Sciences, Lyo-Lab & Process and Chemistry & Consumable. Spinco is proud of its 33 years long partnership with Shimadzu, a global leader in ana-lytical instrumentation. Installation of more than 18000 Shimadzu HPLC across the country is our greatest mile-stone and is a testimony to their leadership in the chromatography market. Standing tall in the Mass Spectrometry market is an exciting range of routine Single-Quad MS to the top of the rung Axima series of MALDI-TOF-TOF including the new generation IT-TOF and Ultra-Fast Triple Quad - all from Shimadzu.

SENSATION ANIMATIONS.N.S Animations which founded by Mr. Shaik Khaja in 2015, works on blending mod-ernist design principles, commercial acumen and real technological expertise to deliv-er inspirational ideas and beautifully crafted designs. Their skills are diverse and their work is driven by comprehensive, interactive designs. When they started their compa-ny, their first project was with Prof. Sanjeeva Srivastava, IIT Bombay for an International Proteomics Conference in 2015, wherein they also bagged the best designer award. Further, they worked on a documentary video project and their work is also uploaded on the HUPO (Human Proteome Organization) website. With their avant-garde digital technologies, they are able to cater to all kinds of digital advertising needs.URL: https://snsanim.wordpress.com/

OTHER SPONSORS

GE HEALTHCARE GE Healthcare provides technologies and services that are shaping a new age of health-care. Our broad expertise in medical imaging and information technologies, medical


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diagnostics, patient monitoring systems, drug discovery, biopharmaceutical manufacturing technologies, perfor-mance improvement and performance solutions services help our customers to deliver better care to more people around the world at a lower cost. In addition, we partner with healthcare leaders, striving to leverage the global policy change necessary to implement a successful shift to sustainable healthcare system. Our “healthy imagina-tion” vision for the future invites the world to join us on our journey as we continuously develop innovations fo-cused on reducing costs, increasing access and improving quality around the world. Headquartered in the United Kingdom, GE Healthcare is a unit of General Electric Company (NYSE: GE) Worldwide, GE Healthcare employ-eesare committed to serving healthcare professionals and their patients in more than 100 countries. URL: http://www.gehealthcare.com/

NANO TEMPER TECHNOLOGIESNanoTemper Technologies stands for a strong commitment to quality and high-preci-sion instrumentation made in Germany. The extremely experienced and globally oper-ating team of experts focuses strongly on users’ benefits by ensuring maximum efficien-cy for research in pharmaceutical and biotechnology industries, as well as in academic research settings. This high-tech company develops, produces and markets technologies and instruments for biomolecular analytics, from basic to preclinical research. With headquarters inMunich, Germany, and subsidiaries in the UK, Poland, US, Brazil and India, the company is rap-idly expanding worldwide. Among others, NanoTemper has been awarded the German Innovation Award 2012, the Bavarian Export Prize 2013 and the Deutscher Gründerpreis 2014. NanoTemper’s high-quality instruments are based on proprietary and innovative technologies:Email: [email protected]: http://www.nanotemper-technologies.com/

BIO-RADBio-Rad Laboratories, Inc. (NYSE: BIO and BIOb) develops, manufactures, and mar-kets a broad range of innovative tools and services to the life science research and clinical diagnostics markets. Founded in 1952, Bio-Rad has a global team of more than 7,750 employees and serves more than 100,000 research and industry custom-ers worldwide through the company’s global network of operations. Throughout its existence, Bio-Rad has built strong customer relationships that advance scientific research and development efforts and support the introduc-tion of new technology used in the growing fields of genomics, proteomics, drug discovery, food safety, medical diagnostics, and more. Bio-Rad’s Life Science Group develops, manufactures, and markets a wide range of labo-ratory instruments, apparatus, and consumables used for research in functional genomics, proteomics, and food safety. The group ranks among the top five life science companies worldwide, and maintains a solid reputation for quality, innovation, and a longstanding focus on the success of its customers. Bio-Rad’s life science products are based on technologies used to separate, purify, identify, analyze, and amplify biological materials such as proteins, nucleic acids, and bacteria. These technologies include electrophoresis, imaging, multiplex immunoassay, chro-matography, microbiology, bioinformatics, protein function analysis, transfection, amplification, real-time and droplet digital PCR. Bio-Rad products support researchers in laboratories throughout the world.

V PROTEOMICS: VProteomics provides high end proteomics services to researchers and Biognosys ready to use targeted proteomics kit and software.We provide complete support to researcher’s right from experimental design of your proteomics experiment till data analysis and interpretation to facilitate translational research. We have the latest proteomics technology platforms and computational in-frastructure in Green Park, New Delhi to answer many of your routine research questions dealing with:1. Protein identification


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2. Proteome dynamics3. PTM modifications and profiling4. Fluid and tissue protein profiling5. Profiling membrane proteins, secreted proteins and exosomes

6. Protein-protein interactionsV7. Target discovery and validation8. Biomarker discovery and validation9. Protein profiling of microorganismsURL: www.vproteomics.com

Floor Plan

Upcoming Event


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Agarwal Atima, p 39

Bhargava Kalpana, p 52

Bhat Akshay A, p 25

Borras Eva, p 10, 58

Chakraborty Niranjan, p 51

Chakraborty Subhra, p 51

Chiva Cristina, p 10, 58

Datta Uma Sinha, p 39

Gupta Sanjay, p55

Jaiswal Mukesh, p 35

Jadhav Sachin Suresh, p 54

Jhingan Gagandeep, p 52

Kahali Madhurima, p 53

Kaneria Mala, p 55

Kumar Swati, p 25

LaBaer Joshua, p 36, 53

MacLean Brendan, p 10, 58

Menon Saji, p 38

Mishra Sharad, p 21

Nallapeta Sivaramaiah, p 35

Navani Sanjay, p 36

Noronha Santosh, p 38

Patankar Swati, p 54

Patel Sandip Kumar, p 25

Priyadarshini Subhra, p 58

Purwar Rahul, p 54

Rana Rashmi, p 55

Rami Bhadresh, p 55

Rane Shailendra, p 58

Saha Pratip, p 24

Selevsek Nathalie, p 10,58

Shastri Jayanti, p 54

Shelkar Yogesh, p 25

Sirdeshmukh Ravi, p 57

Solanki Rahul, p 36

Sonawala Saloni, p 40,53

Srikanth Rapole, p 56

Srivastava Sanjeeva, p 24, 37

Suryavanshi Amol, p 57

Tatu Utpal, p 51

Thakur Suman S, p 56

Ummanni Ramesh, p 38, 52

Vaidya Susheelendra, p 38

Venkatraman Prasanna, p 36

Zingde Surekha, p 53

Author index


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NOTES


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