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.
|Pratik Jagtap (Chair)||University of Minnesota|
|Hua Ding||The Children’s Hospital of Philadelphia|
|Laura Herring||University of North Carolina at Chapel Hill|
|Joanna Kirkpatrick (Co-chair)||The Francis Crick Institute|
|Vikas Kumar||University of Nebraska Medical Center|
|Mukul Midha||Institute of Systems Biology|
|LeRoy Martin||Waters Corporation|
|Benjamin Neely (Co-chair)||National Institute of Standards and Technology|
|Brett Phinney||University of California Davis|
|Baozhen (Paul) Shan||Bioinformatics Solutions Inc.|
|Paul M. Stemmer||Wayne State University|
|Magnus Palmblad (EB Liaison)||Leiden University Medical Center|
|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.
- July 2018: 2018 PRG Study Announcement
- March 2020: Joanna Kirkpatrick presented an update at the Annual ABRF Conference in Palm Springs, CA.
PRG Activities at the ABRF 2019.
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
- 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
|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)
|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