Proteomics (PRG)

Mission

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.

Questions or interest in joining an ABRF research group? Contact us! 
Please join us for the ABRF Virtual Member Town Hall: Proteomics Standards and Reagents: ABRF Research Groups' Update on July 14th, 2021. Click here for more details. 

Current Membership

Benjamin Neely (Co-chair) National Institute of Standards and Technology
Brett Phinney, (Co-chair) University of California Davis
Laura Herring,  University of North Carolina at Chapel Hill
Joanna Kirkpatrick The Francis Crick Institute
Vikas Kumar, University of Nebraska Medical Center
Mukul Midha, Institute for Systems Biology
LeRoy Martin, Waters Corporation
Magnus Palmblad, Leiden University Medical Center
Daniel Polasky, University of Michigan Medical School
Ben Schulz,  The University of Queensland
Paul Stemmer, Wayne State University
Sue Weintraub  (Executive Board Liaison)University of Texas Health Science Center at San Antonio
Yan Wang, NIH/NIDCR

Studies

1)

PRG 2018: Evaluation of Data-Independent Acquisition (DIA) for Protein Quantification in Academic and Core Facility Settings.

The Proteomics Research Group (ABRF) conducted a study to enable academic and core facilities in using Data-Independent Acquisition (DIA) technology. The PRG provided a test sample, protocols and resources to 62 participants from 20 countries to facilitate the use of DIA. Participants were requested to deposit the raw data.

Timeline:

July 20182018 PRG Study Announcement
August-November 2018: Samples were shipped to requesting laboratories. Protocols were made available for researchers.
January 2019: Participants deposited raw data to a MassIVE FTP account and submit information via a questionnaire about the acquired data.
February 2019: PRG analyzed the deposited data.
March 2019: PRG presented the data as a poster and a presentation at the Annual ABRF Conference in San Antonio, TX.
July 2019: Ben Neely and Joanna Kirkpatrick from PRG presented a webinar on the study at the GenomeWeb/ABRF 2019 webinar series.

March 2020: Joanna Kirkpatrick presented an update at the Annual ABRF Conference in Palm Springs, CA.

PRG Activities at the ABRF 2019.

SW1 Workshop
PRG Presentation
PRG Poster

PRG Activities at the ABRF 2020.

Presentation by Pratik Jagtap at the ABRF 2020 Opening Session: Everything you wanted to know about ABRF Research Groups.

Joanna Kirkpatrick presented an update at the Annual ABRF Conference in Palm Springs, CA.

2)

PRG 2017: Quantification of unidentified low abundance proteins with MS1 data and bioinformatics tools
The 2017 ABRF Proteomics Research Group (PRG) study was a member-only study. In this follow-up of the PRG 2016 study, we attempted to use retention time and accurate mass of peptides with relatively high concentration (500 fmol in 25 ug cell lysate) to help quantify the same peptides in samples with low concentration (20 fmol in 25 ug cell lysate). Four softwares (two open source and two commercial) were used to analyze data set from Orbitrap Fusion, QExactive, and Orbitrap XL instruments.  We are finalizing our findings.

3)

PRG 2016: identification of low abundance proteins in a highly complex sample   
    - 2016 PRG Poster Final 

    - PRG Poster at the 64th Annual Conference of American Society of Mass Spectrometry and Allied Topics at San Antonio, TX.

4)

 

 

 

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 
5) 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)
6) 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)
7) 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)
    - #12882 (383K)
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8) 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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    - # 12707 (93K)
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9) 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)
10) 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)
11) PRG 2006: Relative Protein Quantification
This study was completed in March 2006
    - Scatter Plots 
    - Excel Spreadsheet 
    - ABRF2006 Long Beach, CA Presentation 
    - Study Announcement  (95K)
12) PRG 2005: De Novo Peptide Sequencing
This study was completed in 2005
    - PDF Table (34 Pages) 
    - Excel Spreadsheet 
    - Study Announcement  (15K)
13) PRG 2004: Differentiation of Protein Isoforms
This study was completed in 2004
    - Participant Feedback 
    - Study Description 
14) PRG 2003: Phosphorylation Site Determination
This study was completed in 2003
    - Study Description 
15) 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/)
2) Letter to ProteoMonitor Re: PRG 2005 Study

Membership History

Member NameOrganizationDetails
Dr Tracy M Andacht Centers for Disease Control and Prevention  Member: 02/09 - 04/14
Dr. David Arnott Genentech, Inc.  Chair: 03/02 - 02/03
Member: 01/01 - 03/02
Member: 02/03 - 03/04
Keiryn Bennett Center for Molecular Medicine of the Austrian Academy of Sciences  Member: 01/11 - 04/14
Dr Maureen K. Bunger Proteovations, LLC  Chair: 03/11 - 04/14
Member: 02/09 - 02/11
Cory Bystrom Quest Diagnostics  Member: 03/10 - 04/14
Dr. Allis S. Chien Stanford University  Member: 04/07 - 03/10
Dr. Christopher Colangelo Primary Ion  EB Liaison: 04/14 - 04/15
Dr. Larry Dangott Texas A&M University  Member: 03/10 - 04/14
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 William G Hendrickson Univ. of Illinois, Chicago  EB Liaison: 03/13 - 04/14
Member: 03/13 - 04/14
Dr. Pratik Jagtap University of Minnesota  Chair: 07/18 - 07/20
Member: 03/14 - 12/20
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. John Leszyk University of Massachusetts Medical School  Member: 02/11 - 04/14
Dr Kathryn S Lilley University of Cambridge  Member: 05/07 - 02/09
Dr. Michael MacCoss University of Washington  Chair: 03/06 - 02/09
Dr Henrik Molina The Rockefeller University  Member: 03/10 - 04/14
Dr. Robert L Moritz Institute for Systems biology  Member: 02/09 - 04/14
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
: 02/11 - 04/14
Dr. Henriette Remmer University of Michigan Chair: 03/14 - 03/16
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
Dr. David L Tabb Vanderbilt University Medical Center  Ad hoc: 01/13 - 04/14
Dr. J. Will Thompson Duke University Proteomics Core  Member: 01/13 - 04/14
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. Yan Wang NIH/NIDCR Chair: 03/16-06/18 
Member: 03/14 - 
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. Jason Williams NIEHS  Member: 01/13 - 04/14
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
 

Publications

  1. PRG 2002
    DP Arnott, M Gawinowicz, RA Grant, WS Lane, LC Packman, K Speicher, K Stone
  2. PRG 2003
    D Arnott, MA Gawinowicz, RA Grant, TA Neubert, LC Packman, KD Speicher, K Stone, CW Turck
  3. PRG 2004
    D Arnott, MA Gawinowicz, JA Kowalak, WS Lane, KD Speicher, CW Turck, KA West, TA Neubert
  4. PRG 2005
    AM Falick, JA Kowalak, WS Lane, BS Phinney, CW Turck, ST Weintraub, KA West, TA Neubert
  5. PRG 2006
    CW Turck, AM Falick, JA Kowalak, WS Lane, KS Lilley, BS Phinney, ST Weintraub, HE Witkowska, NA Yates
  6. PRG 2007
    AM Falick, WS Lane, KS Lilley, MJ MacCoss, BS Phinney, NE Sherman, ST Weintraub, HE Witkowska, NA Yates
  7. PRG 2008, 2009 & 2010
    DB Friedman, TM Andacht, MK Bunger, AS Chien, DH Hawke, J Krijgsveld, WS Lane, KS Lilley, MJ MacCoss, RL Moritz, RE Settlage, NE Sherman, ST Weintraub, HE Witkowska, NA Yates, CW Turck

 

Questions or interest in joining an ABRF research group? Contact us