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 2018: *2018 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) - #15128 (15K) - #19055 (43K) - #20742 (20K) - #24480 (100K) - #32365 (199K) - #49441 (156K) - #63103 (17K) - #40003
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) - # 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)
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

Electronic Posters

1)	ABRF2013_Presentation
2)	ABRF2013_Poster
3)	ABRF-PRG2011: The Interaction Between Users and Suppliers of Proteomics Services/Facilities
4)	ABRF-PRG2010: Tackling Unforeseen Problems in Otherwise 'Straight-Forward' Proteomics Analyses
5)	ABRF-PRG2009: Relative Protein Quantification in a Clinical Matrix
6)	ABRF-PRG2008: Qualitative Proteomics Study - Identifying Differences in Primary Structure
7)	ABRF-PRG2007: Advanced Quantitative Proteomics Study
8)	ABRF-PRG2006: Relative Protein Quantification
9)	ABRF-PRG2005: De Novo Peptide Sequence Determination
10)	ABRF-PRG2004: Differentiation of Protein Isoforms
11)	ABRF-PRG2003: Phosphorylation Site Determination
12)	ABRF-PRG2002: Identification of Proteins in a Simple Mixture

Membership History

Member Name	Organization	Details
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