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| Proteome Informatics Research Group (iPRG) |
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Current Members |
Studies |
Membership History |
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| The iPRG has announced its 2008/09 study! The new study is focused on finding qualitative (not quantitative) differences between proteins across multiple samples. See below for details! |
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| 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 BIC 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. |
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| Current Membership |
Brian C. Searle
(Chair) - Proteome Software Inc.
Manor Askenazi
- Dana-Farber Cancer Institute
William S. Lane
- Harvard University
Dr. Lennart Martens
- EMBL-EBI
Karen Meyer-Arendt
- University of Colorado
Dr. Alexey I Nesvizhskii
- University of Michigan
Dr. Paul A Rudnick
- NIST
Dr. Sean L. Seymour
- Applied Biosystems
Dr. David L Tabb
- Vanderbilt University Medical Center
Dr Jeffrey A Kowalak
(EB Liaison) - NIMH
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| Studies |
| 1) |
iPRG2009 Study - Announcement
The iPRG invites you to participate in a collaborative study focusing on the evaluation of proteomics laboratories in determining the significantly different proteins between two complex samples. In this study, datasets representing five technical replicates of each sample will be provided, enabling participants to evaluate reproducibility of differences. This study will enable participants to evaluate their capabilities and approaches relative to others in analyzing a common data set. Requests to participate must be submitted by e-mail to iPRG2009@gmail.com prior to Monday, October 20th, 2008. Please see linked file for details!
- View Document
(131K)
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| 2) |
iPRG2008 Study - Initial Results Presentation at ABRF2008
- ABRF2008 Poster
(2,055K)
- ABRF2008 Slides
(728K)
- ABRF2008 ASMS Poster
(890K)
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| 3) |
iPRG2008 Study Materials
- 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)
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| 4) |
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)
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| Membership History |
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