ABRF : Research Groups

Proteomics Research Group (PRG)

PRG 2010 Study now open.

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. David B. Friedman (Chair) - Vanderbilt University
Dr Tracy M Andacht - Centers for Disease Control and Prevention
Dr Maureen K. Bunger - RTI International
Dr. Allis S. Chien - Stanford University
Dr. David Hawke - UT MD Anderson Cancer Center
Jeroen Krijgsveld - EMBL
Dr. Robert L Moritz - Institute for Systems biology
Dr Robert E Settlage - Virginia Bioinformatics Institute
Chris W Turck (EB Liaison) - Max Planck Institute of Psychiatry

Studies

1)	PRG 2010 Proteomics Study 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
2)	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
3)	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)
4)	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)
5)	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)
6)	PRG 2006: Relative Protein Quantification This study was completed in March 2006 - Scatter Plots - Excel Spreadsheet - ABRF2006 Long Beach, CA Presentation - Study Announcement (95K)
7)	PRG 2005: De Novo Peptide Sequencing This study was completed in 2005 - PDF Table (34 Pages) - Excel Spreadsheet - Study Announcement (15K)
8)	PRG 2004: Differentiation of Protein Isoforms This study was completed in 2004 - Participant Feedback - Study Description
9)	PRG 2003: Phosphorylation Site Determination This study was completed in 2003 - Study Description
10)	PRG 2002: Identification of Proteins in a Simple Mixture This study was completed in 2002 - Study Description

Activities

1)	Letter to ProteoMonitor Re: PRG 2005 Study - View Document (51K)

Electronic Posters

1)	ABRF-PRG2009: Relative Protein Quantification in a Clinical Matrix - View Document (429K)
2)	ABRF-PRG2008: Qualitative Proteomics Study - Identifying Differences in Primary Structure - View Document (203K)
3)	ABRF-PRG2007: Advanced Quantitative Proteomics Study - View Poster as PDF
4)	ABRF-PRG2006: Relative Protein Quantification - View Poster as PDF
5)	ABRF-PRG2005: De Novo Peptide Sequence Determination - View Poster as PDF (79K)
6)	ABRF-PRG2004: Differentiation of Protein Isoforms - View Poster as PDF
7)	ABRF-PRG2003: Phosphorylation Site Determination - View Poster as PDF
8)	ABRF-PRG2002: Identification of Proteins in a Simple Mixture - View Poster as PDF (365K)

Publications

1)	ABRF-PRG2006: Relative Protein Quantification - View Document (447K)
2)	ABRF-PRG2005: De Novo Peptide Sequence Determination - View Document (1,132K)
3)	ABRF-PRG2004: Differentiation of Protein Isoforms - View Document (619K)
4)	ABRF-PRG2003: Phosphorylation Site Determination - View Document (693K)
5)	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. Arnold M. Falick	HHMI-UC Berkeley	Chair: 03/06 - 04/07 Member: 03/04 - 02/06
Dr. David B. Friedman	Vanderbilt University	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 Jeffrey A Kowalak	NIMH	Member: 02/03 - 03/06
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
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. 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
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