Targeted Mass SpecEnvironment

On year 9

Brendan MacLean

Viral Growth?Ju

n - 2

011

Jul -

201

1Au

g - 2

011

Sep

- 201

1O

ct -

2011

Nov

- 20

11De

c - 2

011

Jan

- 201

2Fe

b - 2

012

Mar

- 20

12Ap

r - 2

012

May

- 20

12Ju

n - 2

012

Jul -

201

2Au

g - 2

012

Sep

- 201

2O

ct -

2012

Nov

- 20

12De

c - 2

012

Jan

- 201

3Fe

b - 2

013

Mar

- 20

13Ap

r - 2

013

May

- 20

13Ju

n - 2

013

Jul -

201

3Au

g - 2

013

Sep

- 201

3O

ct -

2013

Nov

- 20

13De

c - 2

013

Jan

- 201

4Fe

b - 2

014

Mar

- 20

14Ap

r - 2

014

May

- 20

14Ju

n - 2

014

Jul -

201

4Au

g - 2

014

Sep

- 201

4O

ct -

2014

Nov

- 20

14De

c - 2

014

Jan

- 201

5Fe

b - 2

015

Mar

- 20

15Ap

r - 2

015

May

- 20

15Ju

n - 2

015

Jul -

201

5Au

g - 2

015

Sep

- 201

5O

ct -

2015

Nov

- 20

15De

c - 2

015

Jan

- 201

6Fe

b - 2

016

Mar

- 20

16Ap

r - 2

016

May

- 20

16Ju

n - 2

016

Jul -

201

6Au

g - 2

016

Sep

- 201

6O

ct -

2016

Nov

- 20

16De

c - 2

016

Jan

- 201

7Fe

b - 2

017

Mar

- 20

17Ap

r - 2

017

0

2000

4000

6000

8000

10000

12000

14000

Month - Year of Sign up

Cumulative Skyline Website Registrations from 2011 - to Present

Cuml Active Users

Cuml Active + No Confirm Users

Cuml Active Users + No Confirm +Temp Users

FirstUser Meeting ??

Teaching Targeted Proteomics 3 weeklong courses 2014 Zurich, Seattle, Barcelona

7 workshops and short courses in 2014 Albuquerque, Seattle, Baltimore, Brixen, Seoul, Kyoto, Mumbai

5 weeklong courses 2015 Seattle, Boston, Zurich, Barcelona, Mumbai

5 workshops and short courses in 2015 Tempe, St. Louis, Rio de Janiero, Puerto Vallarta, Tokyo

5 weeklong courses 2016 Zurich, San Francisco, Boston, Seattle, Barcelona

3 workshops and short courses in 2016 Boston, Brixen, Johannesburg

5 weeklong courses 2017 San Francisco, Boston, Zurich, Seattle, Barcelona

3 workshops and short courses in 2017 San Diego, Indianapolis, Dublin

14 Tutorials (9 translated)Method Editing Method Refinement

Existing Experiments

CE Optimization

MS1 Filtering Targeted MS/MS (PRM)

Custom Reports Advanced Peak Picking iRT

Growing…

DIA with DDA

Grouped Studies Small Molecule

15 webinars

Webinar Statistics

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1400

1600

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Total webinar pageviews

Webinar Statistics

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Webinar Pageview Traffic(Monthly since series inception)

Webinar1 - DDA Webinar2 - DIA Webinar3 - PRMWebinar4 - TMD Webinar5 - TMR Webinar6 - ProcessingWebinar7 - iRT Webinar8 - Stats Webinar9 - PTMWebinar10 -Modifications Webinar11 - Panorama Webinar12 - Isotope Labeled StandardsWebinar13 - Calibrated Quantification Webinar14 - Large Scale DIA Webinar 15 - Optimizing Large DIA

2016-2017 Recap – Version 3.6 Improved results import:

Parallel multi-file results import (in user and command-line interfaces) New results import interface for improved unattended imports Greatly improved import performance for Skyline documents on network drives

Calibrated quantification improvements: Surrogate standards for normalizing to explicit non-homologous molecules Remove point right-click option in calibration curve graph Explicit Global Standard Area added to replicates for explicit global normalization control with values like TIC

Group comparison additions and fixes to improve consistency with MSstats New Detection Q Value and Detection Z Score report columns for mProphet scored peak picking New Peak Rank By Level report value and Targets view showing separate peak rankings for MS1 and MS/MS

transitions Peptide uniqueness constraint added to Peptide Settings - Digestion tab (by protein, gene or organism) New Edit > Refine > Associate Proteins for adding protein associations for targeted peptides after they

have been added to the targets list Ability to choose which modifictions to use when showing a library in the Spectral Library Explorer New and improved plots:

Mass error plots (replicate and peptide comparisions and 1D and 2D histograms Multi-peptide retention time plot Point set selection in retention time regression plot

2016-2017 Recap – Version 3.6 (cont.) Improved small molecule support:

Improved support for negative ion mode

Improved chromatogram matching for molecules with identical precursor m/z but different scheduled retention times

Parsing of chemical formula with adduct syntax in Edit > Insert > Transitions

Support for small molecule transition list import with Edit > Paste, File > Import > Transition List, external tools and with command-line

Improved Transition Settings for Full-Scan Centroided extraction with mass error tolerance made default, based on improvement seen with Thermo, Sciex and Bruker instruments

New high-selectivity extraction option (1/2 extraction width) for extraction from profile spectra, based on improvement seen with Termo and Sciex raw data files

Easier import of existing data with improved isolation schemes based on raw data

Fixed support for importing from instruments using different high- and low-resolution between MS1 and MS/MS

Ability to include ambiguously matched spectra in spectral libraries build by Skyline

Improved support for iRT: Support for more iRT standard mixes

Automatic adding of iRT standard targets to document

More flexible iRT regression support (allowing 80% of standards at 0.995 correlation)

CiRT support

SkylineRunner command-line interface improvements: Command-line support for importing transition lists and assay libraries

Command-line support for exporting isolation lists

Command-line support for adding decoy peptides

Improvements made to support AutoQC

mProphet model generation output to console log

Initial support for Sciex MIDAS data

Initial support fixes for Waters SONAR data

Fix for File > Save As bug that disabled Edit > Refine > Re-import

Many other smaller bug fixes

Version 3.7 Coming Soon!

New External Tools Cross-link Transition Calculator

Coming soon… Garuda Integration (pipeline processing with Shimadzu) TraceFinder Integration Lipid Creator

And… MSstats over 10,000 downloads!

What you see is what you believe

See MORE!!with

“WISIATI” – Daniel Kahneman 2011

New Mass Error Graphs Webinar 15 – troubleshooting Bruker data

Mean = 7.8,Standard Deviation = 6.9

-30 -20 -10 0 10 20 30Mass Error (ppm)

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1000

1500

2000

Coun

t

New Mass Error Graphs Webinar 15 – troubleshooting Bruker data

400 600 800 1000 1200 1400m/z

-20

-10

0

10

20

Mas

s Er

ror (

ppm

)

69 24 8 3

New Mass Error Graphs Webinar 15 – Bruker data recalibrated

400 600 800 1000 1200 1400m/z

-20

-10

0

10

20

Mas

s Er

ror (

ppm

)

132 38 11 3

New Multi-Peptide Plots

New Multi-Peptide Plots

New Multi-Peptide Plots

Pan Human DIA: “1 billion peaks”

Reports by Skyline, Plots by R

With Alignment (early)

Reports by Skyline, Plots by R

Pan Human DIA: Peak-only q values

Reports by Skyline, Plots by R

With Alignment (early)

Reports by Skyline, Plots by R

Processing with SkylineRunner NUMA Server (24 cores, 196 GB of RAM) --import-process-count=12 1.5 million transitions (with decoys), 21 files per sit 1 hour per site (11 sites) 5 hours per site on i7 (4 cores) with 32 GB RAM

More Posters to See Brian Pratt – Small Molecule & IMS Nick Shulman – Peak Integration Improvements Josh Eckels – Panorama Abolute Quantification Jarrett Egertson – AWS Automated Pipeline Brian Searle – EncyclopeDIA Progress for Phospho Study

Skyline Team

Nick Shulman

Don Marsh

Brian Pratt

MaxHorowitz-Gelb

Vagisha Sharma

Nat Brace

Kaipo Tamura

Yuval Boss

Collaborators: U. of Wa.

Michael MacCoss Jarrett Egertson Clark Henderson Andy Hoofnagle Lindsay Pinot Brian Searle SoniaTing

Broad Institute Steve Carr Jake Jaffe

Buck Institute Birgit Schilling Brad Gibson

Duke Will Thompson Arthur Moseley

FHCRC Amanda Paulovich Jeffrey Whiteaker

InfoClinika Andrey Bondarenko Oleksii Tymchenko

IMSB Rudolph Aebersold Ben Collins Ludovic Gillet Christina Ludwig Hannes Röst George Rosenburger

LabCorp Chris Shuford Russ Grant

LabKey Josh Eckels

PNNL Erin Baker Yehia Ibrahim Tao Liu Sam Payne

Northeastern Meena Choi Olga Vitek

Stanford Dario Amodei Parag Mallick

Vanderbilt Matthew Chambers

Instrument Vendor Collaborators Agilent Technologies

Christine Miller

Joe Roark

Ed Darland

YinghangYang

Bruker Anette Michalski

Stephanie Kaspar

Pierre-Olivier Schmit

AB Sciex Mark Cafazzo

David Cox

Christie Hunter

Shimadzu Alan Barnes Junko Iida Neil Loftus AtohikoToyama

Thermo-Scientific Susan Abbatiello Andreas Kuehn Rajiv Rawal Jim Shofstahl Vlad Zabrouskov

Waters James Langridge Martin Lunt Keith Richards David Varley Hans Vissers