Skip to main content

Proteomics Research Group (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.

Current Membership

Yan Wang (Chair)University of Maryland
Laura HerringUniversity of North Carolina at Chapel Hill
Pratik D. JagtapUniversity of Minnesota
LeRoy MartinWaters Corporation
Benjamin NeelyNational Institute of Standards and Technology
Brett PhinneyUniversity of California Davis
Baozhen (Paul) Shan Bioinformatics Solutions Inc.
Paul M. StemmerWayne State University 
Allis Chien (EB Liaison)

Stanford University

Studies

1)

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.

2)

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

3)

 

 

 

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 
4)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)
5)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)
6)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)
    - #15128 (15K)
    - #19055 (43K)
    - #20742 (20K)
    - #24480 (100K)
    - #32365 (199K)
    - #49441 (156K)
    - #63103 (17K)
    - #40003 
7)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)
    - # 14850 
    - # 19737 
    - # 21094 
    - # 23300 
    - # 27960 
    - # 41684 
    - # 62904 
    - # 91239 
    - # Unknown 
    - # 12303 
    - # 16131/16132 
    - # 19573 
    - # 26402 
    - # 27406 
    - # 30366 
    - # 47886 
    - # 21970 
    - # 31231 
    - # 46011v1 
    - # 46011v2 
    - # 88007 
    - # 94661 
    - # Unknown2 
    - # 19743 
    - # 50248 
    - # 34364 
    - # 82930 
    - # 93041 
    - # 12107 
    - # 14005 
    - # 12707 (93K)
    - # 14146 (206K)
8)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)
9)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)
10)PRG 2006: Relative Protein Quantification
This study was completed in March 2006
    - Scatter Plots 
    - Excel Spreadsheet 
    - ABRF2006 Long Beach, CA Presentation 
    - Study Announcement (95K)
11)PRG 2005: De Novo Peptide Sequencing
This study was completed in 2005
    - PDF Table (34 Pages) 
    - Excel Spreadsheet 
    - Study Announcement (15K)
12)PRG 2004: Differentiation of Protein Isoforms
This study was completed in 2004
    - Participant Feedback 
    - Study Description 
13)PRG 2003: Phosphorylation Site Determination
This study was completed in 2003
    - Study Description 
14)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 AndachtCenters for Disease Control and Prevention Member: 02/09 - 04/14
Dr. David ArnottGenentech, Inc. Chair: 03/02 - 02/03
Member: 01/01 - 03/02
Member: 02/03 - 03/04
Keiryn BennettCenter for Molecular Medicine of the Austrian Academy of Sciences Member: 01/11 - 04/14
Dr Maureen K. BungerProteovations, LLC Chair: 03/11 - 04/14
Member: 02/09 - 02/11
Cory BystromQuest Diagnostics Member: 03/10 - 04/14
Dr. Allis S. ChienStanford University Member: 04/07 - 03/10
Dr. Christopher ColangeloPrimary Ion EB Liaison: 04/14 - 04/15
Dr. Larry DangottTexas A&M University Member: 03/10 - 04/14
Dr. Arnold M. FalickHHMI-UC Berkeley Chair: 03/06 - 04/07
Member: 03/04 - 02/06
Dr. David B. FriedmanABRF Chair: 02/09 - 03/10
Member: 05/07 - 02/09
Mary Ann GawinowiczHHMI Columbia Univ Member: 01/01 - 03/04
Raymond GrantProcter & Gamble Co Member: 01/01 - 02/03
Dr. David HawkeUT MD Anderson Cancer Center Chair: 03/10 - 02/11
Member: 02/08 - 03/10
Dr William G HendricksonUniv. of Illinois, Chicago MemberEB Liaison: 03/13 - 04/14
Dr Jeffrey A KowalakNIMH Member: 02/03 - 03/06
Jeroen KrijgsveldEMBL Member: 05/07 - 03/10
William S. LaneHarvard University Member: 05/07 - 02/08
Member: 01/01 - 04/02
EB Liaison: 02/03 - 04/07
Dr. John LeszykUniversity of Massachusetts Medical School Member: 02/11 - 04/14
Dr Kathryn S LilleyUniversity of Cambridge Member: 05/07 - 02/09
Dr. Michael MacCossUniversity of Washington Chair: 03/06 - 02/09
Dr Henrik MolinaThe Rockefeller University Member: 03/10 - 04/14
Dr. Robert L MoritzInstitute for Systems biology Member: 02/09 - 04/14
Dr Thomas NeubertNew York Univ Sch of Med Chair: 03/04 - 02/05
Member: 08/02 - 03/04
Dr Len PackmanCambridge University EB Liason: 01/01 - 12/02
Dr. Brett S PhinneyProteomics Core UC Davis Genome Center Member: 03/04 - 04/07
: 02/11 - 04/14
Dr. Henriette RemmerUniversity of MichiganChair: 03/14 - 03/16
Dr Robert E SettlageVirginia Bioinformatics Institute Member: 02/08 - 02/11
Dr. Nicholas E. ShermanUniversity of Virginia Member: 02/06 - 02/09
Kaye D. SpeicherThe Wistar Institute Chair: 02/03 - 03/04
Member: 01/01 - 02/03
Kathy StoneYale Univ Chair: 01/01 - 03/02
Member: 03/02 - 02/03
Dr. David L TabbVanderbilt University Medical Center Ad hoc: 01/13 - 04/14
Dr. J. Will ThompsonDuke University Proteomics Core Member: 01/13 - 04/14
Chris W TurckMax Planck Institute of Psychiatry Chair: 02/05 - 02/06
Member: 03/02 - 02/05
EB Liaison: 04/07 - 02/11
Dr. Susan T. WeintraubUniv. of Texas Health Science Center at San Antonio Member: 03/04 - 04/07
Karen A. WestGalson Laboratories Member: 02/03 - 02/05
Dr. Jason WilliamsNIEHS Member: 01/13 - 04/14
Dr H. Ewa WitkowskaUCSF Member: 02/05 - 02/08
Dr. Nathan A YatesMerck & 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
Back to Top