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

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.

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. 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.

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 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) 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) 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 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
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– # Unknown2
– # 19743
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– # 12107
– # 14005
– # 12707 (93K)
– # 14146 (206K)

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) PRG 2006: Relative Protein Quantification

This study was completed in March 2006 – Scatter Plots
– Excel Spreadsheet
– ABRF2006 Long Beach, CA Presentation
– Study Announcement  (95K) PRG 2005: De Novo Peptide Sequencing

This study was completed in 2005

– PDF Table (34 Pages)
– Excel Spreadsheet
– Study Announcement  (15K) PRG 2004: Differentiation of Protein Isoforms

This study was completed in 2004

– Participant Feedback
– Study Description PRG 2003: Phosphorylation Site Determination

This study was completed in 2003

– Study Description PRG 2002: Identification of Proteins in a Simple Mixture

This study was completed in 2002

– Study Description PRG 2002: Identification of Proteins in a Simple Mixture

This study was completed in 2002

– Study Description

“ABRF and its Research Group Studies” presentation (in German) at ‘Micromethods in Protein Chemistry 2011’ meeting, Munich (http://www.arbeitstagung.de/)

Letter to ProteoMonitor Re: PRG 2005 Study