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AOAPO Newsle�er: 2016, No.1

h�p://www.aoapo.org/Default.aspx

Plant/Crop proteomics Food proteomics

Animal proteomics Microbial proteomics

Inside this issue:

Message from the AOAPO President 2

The Proteomics and Mass Spectrometry Core at the University

of Florida

3

Editor’s notes 6

Proteome Databases Constructed by Members of AOAPO 5

Newsle+er 2016 No 1

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AOAPO Newsle�er: 2016, No.1

Welcome to AOAPO! It is my great honor to serve

as the president in AOAPO. I have seen great

growth in this fine organiza*on since 2010.

Food security has become a priority concern in

the growing economies of Asia and Oceania. With

a rising popula*on, the challenge of security in

food for the future requires integrated approach-

es to increase agricultural produc*on and cope

with environmental challenges. Proteomics play a

role in addressing the growing demand for food.

To promote agricultural proteomic ac*vi*es in

the Asia and Oceania region, the AOAPO was es-

tablished in 2010 at the second Interna*onal

Symposium on Fron*ers in Agricultural Proteome

Research held in Tsukuba, Japan [1]. AOAPO ac-

*vi*es cover a broad range of agricultural proteo-

me research areas including crop, food, insect,

microbial, and animal proteomics.

AOAPO plans to con*nue its support for holding

regular interna*onal symposia in the Asia and

Oceania region. Symposia have already been held

seven *mes in Japan, China, and Korea. The com-

ing symposia are scheduled for India (2016), Ma-

laysia (2017) and Japan (2018). Furthermore, we

have organized the special issue on agricultural

proteomic research in Journal Proteome Research

[2]. The review on “Proteomics of Important Food

Crops in the Asia Oceania Region” has also been

published with corrobora*on of AOAPO Council

[3]. It is expected that similar achievements will

be repeated in the future.

I want to devote my energies to the expansion of

the proteomic research of the agricultural sector.

I believe that our knowledge and experience on

proteomic research will contribute to the

strengthening of AOAPO. I hereby cordially invite

all researchers involved in agricultural proteomics

to join us in this AOAPO endeavor.

Message from the AOAPO President

References:

(1) Komatsu S, Haynes PA, Salekdeh GH. Pro-

mo*ng agriculture proteome research ac*vi*es in

the Asia and Oceania region. J. Proteome Res.

2012, 11:1461.

(2) Komatsu S, Haynes PA. Realizing the poten*al

of agricultural and environmental proteomics. J.

Proteome Res. 2013, 12:4651.

(3) Chakraborty S, Salekdeh GH, Yang P, Woo SH,

Chin CF, Gehring C, Haynes PA, Mirzaei M, Ko-

matsu S. Proteomics of Important Food Crops in

the Asia Oceania Region: Current Status and Fu-

ture Perspec*ves. J. Proteome Res. 2015, 4:2723-

2744.

Professor Setsuko Komatsu

(Na*onal Ins*tute of Crop Science, Japan)

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AOAPO Newsle�er: 2016, No.1

Proteomics and Mass Spectrometry Core at University of Florida

With proteomics and mass spectrometry you can achieve

fast, accurate, high throughput biomolecular separa*on and

characteriza*on, which are indispensable towards under-

standing the biological and medical systems.

Studying at the protein level allows researchers to inves*gate

how proteins, their dynamics, modifica*ons and interac*ons

affect cellular processes. Likewise, it allows researchers to

inves*gate how cellular processes and environment affect

proteins.

The Proteomics and Mass Spectrometry Core at Interdiscipli-

nary Center for Biotechnology Research (ICBR) at University

of Florida has a long history and excep*onal experience in

providing superb proteomics and mass spectrometry services

to customers from University of Florida, USA and around the

world.

We aim to enhance biomedical research and development,

and train and educate scien*sts and students on state-of-the

-art proteomics and mass spectrometry technologies.

Our Core lab is well-equipped with state-of-the-art instru-

ments including a variety of 2D gel electrophoresis systems,

laser scanners and a spot picker from BioRad and GE, Off-gel

frac*onator from Agilent, HPLC, and UHPLC systems from

Agilent, Beckman Coulter, Dionex, Eksigent, and Thermo

Scien*fic, and mass spectrometers from AB Sciex (QSTAR XL,

QSTAR Elite, 4000 QTRAP, and 4700 TOF/TOF), Agilent (QQQ

6495), and Thermo Scien*fic (LCQ Deca, LTQ-Orbitrap, and Q

-Exac*ve Plus) (Figure 1).

In addi*on to keeping our instruments current, we have a

suite of soNware packages (e.g., Progenesis same spot,

DeCyder, Mascot, ProteinPilot, Proteome Discoverer, Prote-

oIQ, Sieve, Scaffold Q+S, Scaffold PTM, Peaks, Pinpoint, and

MRM Pilot) for proteomics and metabolomics analyses.

Figure 1. Major instruments housed in the Proteomics and Mass Spectrometry Core at University of Florida.

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AOAPO Newsle�er: 2016, No.1

Proteomics and Mass Spectrometry Core at University of Florida

(cont.)

The Core has a great team of scien*sts with many years of

experience in proteomics, mass spectrometry, analy*cal

chemistry, and informa*cs (Figure 2). We provide services in

many different areas of biomolecular analyses: 1) high cover-

age protein iden*fica*on; 2) quan*ta*ve proteomics using

gel-based 2D-DIGE, gel-free iTRAQ® and TMT, as well as label-

free quan*fica*on using spectral coun*ng and pep*de peak

areas; 3) protein pos�ransla*onal modifica*on analyses; 4)

sample separa*on/frac*ona*on and protein deple*on or

enrichment; 5) accurate molecular weight analysis; 6) protein

interac*on/complex analysis; and 7) targeted metabolite

profiling.

Our Core is constantly developing new technologies to keep

up with the advancement in the field and customer needs.

For example, a cysTMTRAQ was developed to measure

changes of protein redox modifica*ons and protein levels

simultaneously. In addi*on, protein N-terminal and C-

terminal sequencing methods using mass spectrometry were

recently developed as part of the Core’s involvement in ABRF

studies.

To ensure success and produc*vity along with a great cus-

tomer experience, the Core offers educa*onal workshops,

consulta*on, data processing and repor*ng, and support

with grant applica*ons. Please visit the Core website: h�p://

www.biotech.ufl.edu/proteomics or contact Proteomics and

Mass Spectrometry at University of Florida: ICBR-

Proteomics@ad.ufl.edu.

Figure 2. Team Members of the Proteomics and Mass Spectrometry Core at University of Flori-

da. Front row (leN to right): Ran Zheng (Chemist), Dr. Jin Koh (Scien*fic Director), Ning Zhu

(Biological Scien*st). Back row (leN to right): Dr. Cecilia Silva-Sanchez (Senior Chemist), Leo Zhu

(Technician), Dr. Sixue Chen (Faculty Director).

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AOAPO Newsle�er: 2016, No.1

Proteome Databases Constructed by Members of AOAPO

By the group of Prof. Ghasem Hosseini Salekdeh

About 75% of plant yield poten*al has been es*-

mated to be lost to environmental stresses, even in

developed agricultures. To facilitate the biotechno-

logical improvement of crop produc*vity, genes

and proteins that control crop adapta*on to a wide

range of environments will need to be iden*fied.

Due to the challenges faced in text/data mining,

there is a large gap between the data available to

researchers and the hundreds of published plant

stress proteomics ar*cles. Plant stress proteome

database is an open online proteomic resource,

which currently (as of October 2015) comprises

>20,413 entries from 456 manually curated ar*-

cles, and contains >10,600 unique stress respon-

sive proteins. Since every aspect of the experi-

ments, including protein name, accession number,

plant type, *ssue, stress types, organelles, and de-

velopmental stage has been digi*zed, experi-

mental data can be rapidly accessed and integrat-

ed. Furthermore, PlantPReS enables researchers to

perform mul*ple analyses on the database using

the filtra*on mode, and the results of each query

indicate a series of proteins for which a set of se-

lected criteria is met. The query results can be dis-

played in either text or graphical format.

By the group of Prof. Setsuko Komatsu

The Soybean Proteome Database stores data of

soybean proteins obtained from gel-based and gel-

free proteomic approaches. The goal of the data-

base is to provide proteomic informa*on for func-

*onal analyses. The majority of the data is focused

on soybean, which is an important crop to supply

vegetable oil and protein but is oNen affected by

environmental stresses such as drought, salt, and

flooding. This database was originally constructed

using data of soybean proteins separated by two-

dimensional polyacrylamide gel electrophoresis,

which is referred to as gel-based proteomic ap-

proach. Since 2015, this database has been im-

proved with data by liquid chromatography mass

spectrometry-based label-free quan*ta*ve prote-

omics, which is referred to as gel-free proteomic

approach. As to the label-free proteomics data,

39,212 proteins from 63 sample sets are included,

e.g., temporal and organ specific soybean proteins

without or with flooding stress. Addi*onally, orga-

nelle proteins iden*fied in separated mitochon-

dria, nucleus, and endoplasmic re*culum frac*ons

are stored. Furthermore, the database integrates

mul*ple omics data sets such as genomic, tran-

scriptomic, and metabolomic data. The whole da-

tabase is coordinated based on a scheme of differ-

en*al omics to iden*fy *me-variant proteins under

flooding stress.

PlantPReS: Plant Stress Proteome Data-

base

h�p://www.proteome.ir/

SPD: Soybean Proteome Database

h�p://proteome.dc.affrc.go.jp/Soybean/

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AOAPO Newsle�er: 2016, No.1

Editor’s notes

It is my pleasure to bring to you the first issue of

the AOAPO newsle�er for the year 2016. The

AOAPO newsle�er will be published biannually.

For millennia, humans have relied on agriculture

for food and survival. As technology advances,

tremendous changes have been brought to our

lives which have increased our comfort and

lifespan. However, as the world popula*on expo-

nen*ally grows, we are faced with challenges

such as the danger of food shortages which

might bring catastrophe to our future genera-

*ons. Here, in AOAPO, we are a small group of

scien*sts from the Asia Oceanic region working

hard to use the latest cuXng edge technology in

proteomics in order to unravel the biological and

cellular mechanisms in animals and crops grow-

ing in our regions to help circumvent the impend-

ing challenges.

In this issue, we present to you the welcoming

message from our President, Prof Setsuko

Kotmasu, a renowned proteomic scien*st from

the Na*onal Ins*tute of Crop Science, Japan. We

also take a glimpse into the Proteomics and Mass

Spectrometry Core at the Interdisciplinary Center

for Biotechnology Research (ICBR) at the Univer-

sity of Florida. The Proteomics and Mass Spec-

trometry Core Faculty director, Prof Sixue Chen,

provided us with a brief descrip*on of the prote-

omic instruments and facili*es in the center. . In

addi*on, we also brought to you two proteome

databases constructed by our AOAPO members

on plant proteins related to the environmental

stress.

We hope that you find the informa*on in our

newsle�er useful and we look forward to seeing

you in New Delhi, India in our next AOAPO sym-

posium in December 2016.