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Proteome Informatics Research Group (iPRG)

Mission

The mission of the ABRF iPRG (formerly the BioInformatics Committee) is to educate ABRF members and the scientific community on best application and practice of bioinformatics toward accurate and comprehensive analysis of proteomics data. The iPRG actively supports and participates in the development and advancement of new algorithms, software tools and strategies for proteome informatics with the goal of both educating and introducing these technologies to the membership.

Current Membership

Darryl Davis (Co-Chair) - Janssen Pharmaceuticals, Horsham, PA
Magnus Palmblad (C0-Chair) - Leiden University Medical Center, Netherlands   
Michael Hoopmann - Institute for Systems Biology, Seattle, WA 
Susan T. Weintraub - Univ. of Texas Health Science Center at San Antonio 
Hyungwon Choi - National University of Singapore
Samuel Payne - Pacific Northwest National Laboratory, Richland, WA
Lukas Käll - Royal Institute of Technology, Stockholm, Sweden
Yasset Perez-Riverol - European Bioinformatics Institute, Hinxton, UK
Christopher Colangelo (EB Liaison) - Primary Ion

Studies

1)  iPRG 2018/2019 Study: Details coming soon!
2)  iPRG 2016/2017 Study: Inferring Proteoforms from Bottom-up Proteomics Data. Participants were given raw data and a sequence file, and asked to identify the proteins and provide estimates on the false discovery rate on the proteoform level. As part of this study, a new submission system with a format validator running on a virtual private server (VPS) and allowing methods to be provided as executable R Markdown or IPython Notebooks was introduced and tested.
    - 2016/2017 Study website, including instructions.
    - 2016/2017 Study-related paper in J. Proteome Res.
    - 2016/2017 Study design and outcome manuscript submitted to JBT.
3)  iPRG 2015 Study: Differential Abundance Analysis in Label-Free Quantitative Proteomics. This study of LC-MS/MS data analysis focuses on data processing and statistical assessment for relative protein-level quantification in label-free proteomics.
    - Instructions  (335K)
    - Study letter  (177K)
    - Original iPRG 2015 Presentation Slides  (4,922K)
4)  iPRG 2013 Study: Using RNA-Seq Data to Refine Proteomic Data Analysis. This study evaluates the benefits of using databases derived from RNA-Seq data for peptide identification. Initial results from this study were presented at the annual conference on 2-5 March 2013. Links to poster and slide presentations are below.
    - Study Flyer (145K)
    - Study Participation Letter  (66K)
    - iPRG2013 Poster presented at ABRF Conference  (2,320K)
    - iPRG2013 Slides presented at ABRF Conference 
5)  iPRG2012 Study: Detecting Modified Peptides in a Complex Mixture. This study was presented at the annual ABRF conference in Orlando, FL from March 17th-20th. Poster and Powerpoint presentations of the results are available below, along with the consensus peptide identifications for all spectra. In addition, all data, including raw file, peaklists in various formats, protein databases and Excel spreadsheet containing all participant’s results including consensus assignments and scripts and instructions for how someone can add and compare their own results to those submitted during the study can be downloaded from the following ftp site: Servername:ftp.peptideatlas.org; Username: iprg_public; Password: ABRF
    - iPRG2012 Study Participation Letter 
    - iPRG 2012 Poster (2,207K)
    - iPRG 2012 study annotated consensus spreadsheet  (1,639K)
    - iPRG2012 Powerpoint Presentation  (1,933K)
6)  iPRG 2011 Study: Identification of Electron Transfer Dissociation (ETD) Mass Spectra. The updated slides contain some footnotes, slightly better positioned graphs here and there, and the addition of one extra participant, whose original contribution had been lost in the mail spam filter.
    - View iPRG 2011 Study Announcement  (140K)
    - Original iPRG 2011 Presentation Slides 
    - Updated iPRG 2011 Presentation Slides  (6,529K)
    - iPRG 2011 study annotated consensus spreadsheet  (8,797K)
    - Original iPRG 2011 Poster  (254K)
7)  iPRG 2010 Study: Phosphopeptide Identification. The Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) performed a collaborative data analysis study focusing on the evaluation of proteomics laboratories in identifying phosphopeptides and localizing the phosphorylation sites. In this study, an LC-MS/MS dataset from a lysate digested with trypsin and enriched for phosphopeptides using strong cation exchange fractionation followed by immobilized metal affinity chromatography (SCX/IMAC) will be provided. This study will enable participants to evaluate their data analysis capabilities and approaches relative to others in analyzing a common data set.
    - View Request for Participation 
    - ABRF2010 Presentation Slides  (1,825K)
    - ABRF2010 Poster (239K)
    - ABRF2010 Consensus Results Spreadsheets 
8)  iPRG2009 Study - Initial Results Presentation at ABRF2009
Determining significant differences between mass spectrometry datasets from biological samples is one of the major challenges for proteome informatics. The ability to determine protein level differences is the first step towards accurate quantitation and is routinely used in tasks such as biomarker discovery. In this work, the Proteome Informatics Research Group presents the results of a collaborative study focusing on the determination of significantly different proteins between two complex samples.
    - ABRF2009 Presentation Slides  (2,683K)
    - ABRF2009 Poster (1,467K)
    - iPRG2009 Answer Key (150K)
9)  iPRG2009 Study Materials
The iPRG has conducted a collaborative study focusing on the evaluation of proteomics laboratories in determining the significantly different proteins between two complex samples. These files were distributed to participants to help standardize results.
    - Study Announcement (.pdf) 
    - Required Excel Results Template (.xls) 
    - Required Study Database (1.7MB .fasta) 
10)  iPRG2008 Study - Initial Results Presentation at ABRF2008
    - ABRF2008 Poster  (2,055K)
    - ABRF2008 Slides  (728K)
    - ABRF2008 ASMS Poster  (890K)
    - iPRG2008 Answer Key (616K)
    - iPRG2008 Study Participation Letter  (251K)
11)  iPRG2008 Study Materials. If it asks for a password when unzipping a file, the password should be 'iprgcode'.
    - View Study Announcement  (23K)
    - Study database with concatenated decoys (fixed) (30,485K)
    - Study database (fixed 15.9 M) 
    - MGF format peak list set  (5,132K)
    - Raw data - PART1 (33,253K)
    - Raw data - PART2 (30,218K)
    - Raw data - PART3 (25,498K)
    - Raw data - PART4 (28,933K)
    - Raw data - PART5 (26,564K)
    - mzData format peak lists  (7,585K)
    - mzXML format peak lists  (5,332K)
    - DTA format peaklists (16,203K)
    - Required Excel results template  (23K)
12)  sPRG BIC2007 Study
In 2005, the ABRF Proteomics Standards Research Group (sPRG) created a proteomics standard composed of 49 highly purified human proteins in an equimolar mixture. The sPRG conducted a blind study to assess the proteomics community’s ability to determine the identities of the constituent proteins using their proteomics platforms of choice. The results of this study were presented at ABRF 2006 in Long Beach, CA. The study revealed the value of multiple independent analyses of this proteomics standard, and contributors were asked to voluntarily contribute their datasets for future public distribution. Approximately 30 datasets were submitted representing a wide variety of proteomics strategies and mass spectrometry platforms.
The sPRG Bioinformatics Committee (BIC) has analyzed these datasets in detail using a wide variety of informatics tools. Generating a definitive list of protein constituents was our initial goal. In addition, we present metrics for quality assessment from these data, and we demonstrate statistical approaches for determining false positive rates. We also explore the complex issues resulting from protein sequence homology. The ABRF sPRG2006 Proteomics Standard constitutes a valuable dataset for the evaluation of proteome informatics tools.

    - View Press Release - March 2007 
    - View Poster - BIC2007  (1,209K)
    - View Presentation Slides - BIC2007 (4,020K)
    - Download sPRG BIC DB (zipped archive)  (5,547K)
    - Download sPRG BIC Final Protein List  (37K)
    - Download Metadata on sPRG2007 datasets.xls  (18K)
    - Download Original Raw Data (ProteomeCommons.org) 

Activities

 Several participants at the iPRG session on proteomics informatics during the ABRF 2010 meeting have requested access to the presentations given by the three speakers. All three have generously agreed to providing access to their talks as PDF, to which we have added the introductory slides by Chairman Brian Searle. You can find the four PDFs linked below. Enjoy!
    - Introductory slides (Brian Searle) (159K)
    - Peptide identification (John Cottrell) (1,449K)
    - Post-translational modifications (Nuno Bandeira) (1,195K)
    - Protein identification (Sean Seymour) (689K)

Membership History

Member NameOrganizationDetails
Manor AskenaziDana-Farber Cancer Institute Member: 03/08 - 03/11
Nuno BandeiraUniversity of California, San Diego Member: 04/10 - 03/13
Conrad BessantCranfield University Member: 03/09 - 12/09
Christopher Colangelo AgilentMember: Current
Robert J ChalkleyUCSF Chair: 11/11 - 03/13
Member: 04/10 - 10/11
Hyungwon Choi National University of SingaporeMember: Current
Karl ClauserBroad Institute of MIT and Harvard Member: 04/09 - 03/12
Darryl L. DavisJanssenMember: Current
Eric DeutschInstitute for Systems Biology Member: 04/10 - 03/13
Jayson FalknerUniversity of Michigan Member: 12/07 - 12/09
Michael Hoopmann Institute for Systems Biology Member: Current
Lukas Käll Royal Institute of Technology Member: Current
Eugene A. KappWEHI Member: 12/11 - 03/13
Jeffrey A KowalakNIMH EB Liaison: 04/07 - 04/10
Henry H. LamHong Kong University of Science and Technology Ad hoc: 12/10 - 03/11
Member: 04/11 - 10/13
William S. LaneHarvard University Member: 04/07 - 04/10
EB Liaison: 03/06 - 04/07
Lennart MartensGhent University Chair: 04/10 - 03/11
Member: 04/08 - 04/10
W. Hayes McDonaldVanderbilt University Chair: 03/11 - 10/11
Member: 11/11 - 03/12
Member: 03/09 - 03/11
Karen Meyer-ArendtUniversity of Colorado Member: 04/08 - 04/10
Alexey I NesvizhskiiUniversity of Michigan Member: 03/06 - 03/08
Thomas NeubertNew York Univ Sch of Med EB Liaison: 04/10 - 04/14
Member: 04/14 - 04/17
Magnus Palmblad (Chair) Leiden University Medical Center Member: Current
Samuel Payne Pacific Northwest National Laboratory Member: Current
Yasset Perez-Riverol European Bioinformatics Institute Member: Current
Brett S PhinneyProteomics Core UC Davis Genome Center EB Liaison: 04/14 - 04/15
Paul A RudnickNIST Chair: 02/09 - 04/10
Member: 03/08 - 02/09
Member: 04/10 - 03/11
Brian C. SearleProteome Software Inc. Chair: 02/08 - 02/09
Member: 02/09 - 04/10
Member: 03/06 - 02/08
Sean L. SeymourAB SCIEX Chair: 03/06 - 02/08
Member: 02/08 - 02/09
David L TabbVanderbilt University Medical Center Member: 03/06 - 02/09

Susan T. Weintraub  

Univ. of Texas Health Science Center at San AntonioMember: Current
 
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