Proteomics Research Group (PRG)
| Current Members | Studies | Activities | Electronic Posters | Publications | Membership History |

The Proteomics Research Group (PRG) is a volunteer scientific organization dedicated to sharing knowledge about the analysis of proteins. The PRG aims to assist protein scientists and resource facilities to achieve their highest potential by sponsoring annual research studies that examine current techniques and capabilities. Through the promotion of broad participation and scientific excellence, the PRG aims to raise awareness, knowledge and education about modern methods of protein analysis.

Current Membership
Dr Maureen K. Bunger (Chair) - Proteovations, LLC
Keiryn Bennett - Center for Molecular Medicine of the Austrian Academy of Sciences
Dr. Larry Dangott - Texas A&M University
Dr William G Hendrickson (EB Liaison) - Univ. of Illinois, Chicago
Dr. John Leszyk - University of Massachusetts Medical School
Dr Henrik Molina - The Rockefeller University
Dr. Jason Williams - NIEHS
Dr. David L Tabb (Ad hoc) - Vanderbilt University Medical Center
Dr. Christopher Colangelo (EB Liaison) - Yale University
Dr. Brett S Phinney - Proteomics Core UC Davis Genome Center

The PRG is pleased to make available the preliminary results from our 2-year QC study. The exceptional turnout for this study (over 60 participants) was beyond expectations. We intend to make all the processed data available following manuscript submission. Summaries are available in the uploaded poster and talk PDFs. We hope you find the results informative.

Studies
1) PRG 2012: Quality Control LC-MS/MS study
The 2012 ABRF Proteomics Research Group (PRG) is pleased to announce initiation of a study focused on quality control and reproducibility in the proteomics lab. We invite you to participate in this study that will require a commitment of approximately 2 hours, once every month for 9 consecutive months.
    - 2012 PRG Study Announcement (80K)
    - 2012 ABRF conference presentation (927K)
    - 2012 ABRF Conference PRG Poster (649K)
    - 2013 ABRF Conference presentation
    - 2013 ABRF Conference poster
2) PRG 2011 Proteomics Survey:
The Proteomics Research Group has invited interested proteomics laboratory managers, administrators and users to participate in its first Survey Study. Results were presented at the ABRF2011 conference.
    - Survey Announcement (18K)
    - PRG2011 Survey Presentation (1,844K)
3) PRG 2010: Identifying unforeseen problems in otherwise ‘straight-forward’ proteomics analyses
The PRG invites you to participate in a study that explores the use of different approaches for determining sample composition and identifying unforeseen problems in otherwise ‘straight-forward’ proteomics analyses. The PRG will provide the test samples along with sufficient information in a way that is consistent with a real-world sample being submitted to a core facility for analysis. The PRG anticipates that the samples can be successfully characterized by scientists with different levels of experience using a wide variety of proteomic approaches and platforms (e.g. shotgun, top-down, SDS-PAGE, gel free, ESI, MALDI, low resolution, high resolution, etc.) over a relatively short (1-2 week) timeframe. The primary goal of this study is to document the breadth of approaches used by the ABRF community and highlight the type of information obtained. In particular, the study will involve a) several levels of experimental challenges to enable scientists with different levels of experience to assess their abilities, b) submission of results in an on-line survey format, and c) comparison of best practices among respondents.
    - Study Announcement (24K)
    - Study Letter
    - Supplementary Information
    - ABRF2010 PRG Study Presentation (912K)
    - PRG2010 Poster (236K)
    - results write-up (211K)
    - results write-up (23K)
    - results write-up (14K)
4) PRG 2009: Relative Protein Quantification in a Clinical Matrix
A targeted relative protein quantification study relevant for a biomarker validation project. Results from participants were submitted using an on-line survey. In addition, participants were asked to provide a short summary of the approach(es) they used and the key results they obtained (see links below).
    - Study Sample Letter (129K)
    - Study Sample Protein Information
    - Study Announcement Letter (28K)
    - Survey Information
    - Selected Mass Spectrometry Data (86K)
    - PRG2009_Presentation (1,269K)
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5) PRG 2008: Qualitative Proteomics Study Results
Results from participants were submitted using an on-line survey. In addition, participants were asked to provide a short summary of the approach(es) they used and the key results they obtained. The links below lead to the tabulated results and the participants’ (anonymous) individual summaries. The PRG publishes this information so that effective protocols and novel strategies can be readily shared with the proteomics community.
    - Survey Results Table
    - PRG 2008 Presentation (325K)
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6) PRG 2008: Qualitative Proteomics
The current study explores the use of different proteomic approaches for determining qualitative differences between two similar samples. The PRG anticipates that the samples can be successfully characterized by scientists with different levels of experience using a wide variety of proteomic approaches and platforms (e.g. shotgun, top-down, SDS-PAGE, gel free, ESI, MALDI, low resolution, high resolution, etc.). The primary goal of this study is to document the breadth of approaches used by the ABRF community and highlight the type of information obtained by each. Participants will be asked to a) identify the proteins present in two similar samples, b) determine any qualitative differences between the proteins in the samples, and c) provide information about methods used to maximize protein sequence coverage.
    - Study Announcement and Sample Request (36K)
    - Vendor and Commercial Service Lab Guidelines
    - Study Sample Letter (37K)
7) PRG 2007: Advanced Quantitative Proteomics
This study was completed in April 2007 and allowed participating labs to evaluate capabilities and approaches with regard to a) the detection and identification of known proteins present in different amounts in three samples that also contain complex mixtures of background proteins, b) the determination of the relative amounts of the standard proteins in the three samples, c) comparison of the number of correct and incorrect results as an indication of the overall performance of the methodologies used .
    - ABRF2007 Tampa, FL Presentation
    - ABRF2007 Tampa, FL Poster
    - PRG07: Sample letter
    - PRG07: Survey Introduction
    - Optional Submission of PRG2007 Raw Data (26K)
8) PRG 2006: Relative Protein Quantification
This study was completed in March 2006
    - Scatter Plots
    - Excel Spreadsheet
    - ABRF2006 Long Beach, CA Presentation
    - Study Announcement (95K)
9) PRG 2005: De Novo Peptide Sequencing
This study was completed in 2005
    - PDF Table (34 Pages)
    - Excel Spreadsheet
    - Study Announcement (15K)
10) PRG 2004: Differentiation of Protein Isoforms
This study was completed in 2004
    - Participant Feedback
    - Study Description
11) PRG 2003: Phosphorylation Site Determination
This study was completed in 2003
    - Study Description
12) PRG 2002: Identification of Proteins in a Simple Mixture
This study was completed in 2002
    - Study Description

Activities
1) "ABRF and its Research Group Studies" presentation (in German) at 'Micromethods in Protein Chemistry 2011' meeting, Munich (http://www.arbeitstagung.de/)
    - View Document (1,496K)
2) Letter to ProteoMonitor Re: PRG 2005 Study
    - View Document (51K)

Electronic Posters
1) ABRF2013_Presentation
    - View Document (1,442K)
2) ABRF2013_Poster
    - View Document (1,225K)
3) ABRF-PRG2011: The Interaction Between Users and Suppliers of Proteomics Services/Facilities
    - PRG2011 Survey (521K)
4) ABRF-PRG2010: Tackling Unforeseen Problems in Otherwise 'Straight-Forward' Proteomics Analyses
    - View Document (236K)
5) ABRF-PRG2009: Relative Protein Quantification in a Clinical Matrix
    - View Document (429K)
6) ABRF-PRG2008: Qualitative Proteomics Study - Identifying Differences in Primary Structure
    - View Document (203K)
7) ABRF-PRG2007: Advanced Quantitative Proteomics Study
    - View Poster as PDF
8) ABRF-PRG2006: Relative Protein Quantification
    - View Poster as PDF
9) ABRF-PRG2005: De Novo Peptide Sequence Determination
    - View Poster as PDF (79K)
10) ABRF-PRG2004: Differentiation of Protein Isoforms
    - View Poster as PDF
11) ABRF-PRG2003: Phosphorylation Site Determination
    - View Poster as PDF
12) ABRF-PRG2002: Identification of Proteins in a Simple Mixture
    - View Poster as PDF (365K)

Publications
1) ABRF-PRG 2008 2009 2010 studies. Three PRG studies now published in one paper in the Journal Proteomics under "Standardisation and Guidelines". The journal has made the manuscript freely available for download without a subscription, and the manuscript is also highlighted on the journal homepage at www.proteomics-journal.com.
    - Download manuscript
    - manuscript highlight on Journal homepage
2) ABRF-PRG2007: Advanced Quantitative Proteomics
    - View Document (3,501K)
3) ABRF-PRG2006: Relative Protein Quantification
    - View Document (447K)
4) ABRF-PRG2005: De Novo Peptide Sequence Determination
    - View Document (1,132K)
5) ABRF-PRG2004: Differentiation of Protein Isoforms
    - View Document (619K)
6) ABRF-PRG2003: Phosphorylation Site Determination
    - View Document (693K)
7) ABRF-PRG2002: Protein Identification in a Mixture
    - View Document (146K)

Membership History
Member Name Organization Details
Dr. David Arnott Genentech, Inc.  Chair: 03/02 - 02/03
Member: 01/01 - 03/02
Member: 02/03 - 03/04
Dr Maureen K. Bunger Proteovations, LLC  Member: 02/09 - 02/11
Dr. Allis S. Chien Stanford University  Member: 04/07 - 03/10
Dr. Arnold M. Falick HHMI-UC Berkeley  Chair: 03/06 - 04/07
Member: 03/04 - 02/06
Dr. David B. Friedman ABRF  Chair: 02/09 - 03/10
Member: 05/07 - 02/09
Mary Ann Gawinowicz HHMI Columbia Univ  Member: 01/01 - 03/04
Raymond Grant Procter & Gamble Co  Member: 01/01 - 02/03
Dr. David Hawke UT MD Anderson Cancer Center  Chair: 03/10 - 02/11
Member: 02/08 - 03/10
Dr Jeffrey A Kowalak NIMH  Member: 02/03 - 03/06
Jeroen Krijgsveld EMBL  Member: 05/07 - 03/10
William S. Lane Harvard University  Member: 05/07 - 02/08
Member: 01/01 - 04/02
EB Liaison: 02/03 - 04/07
Dr Kathryn S Lilley University of Cambridge  Member: 05/07 - 02/09
Dr. Michael MacCoss University of Washington  Chair: 03/06 - 02/09
Dr Thomas Neubert New York Univ Sch of Med  Chair: 03/04 - 02/05
Member: 08/02 - 03/04
Dr Len Packman Cambridge University  EB Liason: 01/01 - 12/02
Dr. Brett S Phinney Proteomics Core UC Davis Genome Center  Member: 03/04 - 04/07
Dr Robert E Settlage Virginia Bioinformatics Institute  Member: 02/08 - 02/11
Dr. Nicholas E. Sherman University of Virginia  Member: 02/06 - 02/09
Kaye D. Speicher The Wistar Institute  Chair: 02/03 - 03/04
Member: 01/01 - 02/03
Kathy Stone Yale Univ  Chair: 01/01 - 03/02
Member: 03/02 - 02/03
Chris W Turck Max Planck Institute of Psychiatry  Chair: 02/05 - 02/06
Member: 03/02 - 02/05
EB Liaison: 04/07 - 02/11
Dr. Susan T. Weintraub Univ. of Texas Health Science Center at San Antonio  Member: 03/04 - 04/07
Karen A. West Galson Laboratories  Member: 02/03 - 02/05
Dr H. Ewa Witkowska UCSF  Member: 02/05 - 02/08
Dr. Nathan A Yates Merck & Co. Inc.  Chair: 04/07 - 02/08
Member: 02/05 - 04/07