Proteome Informatics Research Group (iPRG)
| Current Members | Studies | Activities | Membership History |

The 2015 Study is now open BELOW.

The 2012 study is now closed. Results can be found BELOW.

The 2011 study is now closed. Results can be found BELOW.

The 2010 study is now closed, but if you are interested in the results, they can be found BELOW.

For those of you interested in the iPRG session talks at ABRF 2010, please find the PDFs of these talks BELOW.

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
Mr Eugene A. Kapp (Chair) - WEHI
John Cottrell - Matrix Science Ltd
Dr. Michael Hoopmann - Institute for Systems Biology
Dr. Sangtae Kim
Dr Thomas Neubert - New York Univ Sch of Med
Dr. Magnus Palmblad - Leiden University Medical Center
Dr. Olga Vitek - Purdue University
Dr. Susan T. Weintraub - Univ. of Texas Health Science Center at San Antonio
Dr. Henry Lam (Co-Chair) - Hong Kong University of Science and Technology
Dr. Brett S Phinney (EB Liaison) - Proteomics Core UC Davis Genome Center

Studies
1) 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)
2) 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
3) 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)
4) 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)
5) 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
6) 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)
7) 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)
8) 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)
9) 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)
    - 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)
10) 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
1) 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 Name Organization Details
Manor Askenazi Dana-Farber Cancer Institute  Member: 03/08 - 03/11
Nuno Bandeira University of California, San Diego  Member: 04/10 - 03/13
Dr Conrad Bessant Cranfield University  Member: 03/09 - 12/09
Robert J Chalkley UCSF  Chair: 11/11 - 03/13
Member: 04/10 - 10/11
Karl Clauser Broad Institute of MIT and Harvard  Member: 04/09 - 03/12
Dr. Eric Deutsch Institute for Systems Biology  Member: 04/10 - 03/13
Jayson Falkner University of Michigan  Member: 12/07 - 12/09
Mr Eugene A. Kapp WEHI  Member: 12/11 - 03/13
Dr Jeffrey A Kowalak NIMH  EB Liaison: 04/07 - 04/10
Dr Henry H. Lam Hong Kong University of Science and Technology  Ad hoc: 12/10 - 03/11
Dr. Henry Lam Hong Kong University of Science and Technology  Member: 04/11 - 10/13
William S. Lane Harvard University  Member: 04/07 - 04/10
EB Liaison: 03/06 - 04/07
Prof. Lennart Martens Ghent University  Chair: 04/10 - 03/11
Member: 04/08 - 04/10
Dr. W. Hayes McDonald Vanderbilt University  Chair: 03/11 - 10/11
Member: 11/11 - 03/12
Member: 03/09 - 03/11
Karen Meyer-Arendt University of Colorado  Member: 04/08 - 04/10
Dr. Alexey I Nesvizhskii University of Michigan  Member: 03/06 - 03/08
Dr Thomas Neubert New York Univ Sch of Med  EB Liaison: 04/10 - 04/14
Dr. Paul A Rudnick NIST  Chair: 02/09 - 04/10
Member: 03/08 - 02/09
Member: 04/10 - 03/11
Brian C. Searle Proteome Software Inc.  Chair: 02/08 - 02/09
Member: 03/06 - 02/08
Member: 02/09 - 04/10
Dr. Sean L. Seymour AB SCIEX  Chair: 03/06 - 02/08
Member: 02/08 - 02/09
Dr. David L Tabb Vanderbilt University Medical Center  Member: 03/06 - 02/09