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 (Chair) - Janssen Pharmaceuticals, Horsham, PA
Antony Harvey - Thermo Fisher Scientific, Austin, TX
Michael Hoopmann - Institute for Systems Biology, Seattle, WA
Susan T. Weintraub - Univ. of Texas Health Science Center at San Antonio
Samuel H. Payne - Brigham Young University, Provo, UT
Lukas Käll - Royal Institute of Technology, Stockholm, Sweden
Yasset Perez-Riverol - European Bioinformatics Institute, Hinxton, UK
Magnus Palmblad (EB Liaison) - Leiden University Medical Center, The Netherlands
Studies
| 1) | iPRG 2020 Study on Metaproteomics was launched March 31, 2020. Phase 1 concluded July 31. See original invitation and instructions here. For Phase 2 instructions, see here. All are welcome to participate in Phase 2. Participation in Phase 1 is NOT a prerequisite to take part in Phase 2. The deadline for Phase 2 submissions is November 2, 2020. | ||
| 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. | ||
| 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. | ||
| 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. | ||
| 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 | ||
| 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. | ||
| 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. | ||
| 8) | iPRG2009 Study - Initial Results Presentation at ABRF2009 | ||
| 9) | iPRG2009 Study Materials | ||
| 10) | iPRG2008 Study - Initial Results Presentation at ABRF2008 | ||
| 11) | iPRG2008 Study Materials. If it asks for a password when unzipping a file, the password should be 'iprgcode'. | ||
| 12) | sPRG BIC2007 Study |
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
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