Proteome Informatics (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.

Questions or interest in joining an ABRF research group? Contact us! 

Current Membership

Michael Hoopmann (Co-Chair) - Institute for Systems Biology, Seattle, WA
Pratik Jagtap (Co-Chair) - University of Minnesota, Minneapolis, MN
Viktoria Dorfer - University of Applied Sciences, Upper Austria (FH OOE), Hagenberg, Austria
Melanie Föll - University Medical Center Freiburg, Germany
Magnus Palmblad - Leiden University Medical Center, The Netherlands
Yasset Perez-Riverol - European Bioinformatics Institute, Hinxton, UK
Susan T. Weintraub (EB Liaison) - University of Texas Health Science Center at San Antonio

iPRG-2023 Proteome Informatics Research Group Study on Crosslinking
MS Data Analysis

Study Overview 
Crosslinking MS is performed to infer interaction sites between proteins and structural restraints from individual proteins in purified or enriched protein complexes, or the full complement of proteins in a cellular lysate. For most experiments, proteins are chemically crosslinked, enzymatically digested, and analyzed by data-dependent acquisition on a high-performance mass spectrometer. Protein structure restraints and interactions are inferred by the identification of two distinct peptide sequences crosslinked in a tandem mass spectrum derived from a single precursor ion. Although crosslinked peptide analysis is fundamentally the same as typical data-dependent MS peptide analysis, processing pipelines for crosslinked peptide data often require specialized algorithms with parameters and constraints that differ from the more familiar ones employed for traditional protein identification/characterization.

Study Goals 
The goal of this study is to gain information from the proteomics community about the different approaches for crosslinked peptide MS data analysis, showcasing the multitude of different pipelines and tools available, and providing guidance for improving the presentation of crosslinked MS results.

Study Participation
This study is open to everyone. Prior expertise is not required, and tutorials are provided to teach participants new to crosslinking MS. Participants are asked to use one or more database search methods to identify crosslinked residues of protein complexes from data-dependent mass spectrometry data. Two datasets of different protein complexes are provided for which the participants must identify a) the proteins that are crosslinked to each other, b) the specific residues that are crosslinked, and c) the certainty or confidence (e.g., probabilities or q-values) of their conclusions. Details are provided in the study package.


Study Package and Results Submission

The Study Package is available on https://osf.io/ycvw7
To submit results, contact [email protected] to receive access to a private submission portal.

Participants are welcome to submit up to three sets of results for the study. Each submission will be assigned an identifier and private results submission portal. We ask that contact information be provided in case the study committee has follow-up questions. Although results submission is not anonymous, all results will be reported anonymously. Participants may update their submissions via the submission portal at any time until the submission deadline. Results will be final on February 15, 2024.

Important note to corporate partners and commercial laboratories: ABRF imposes strict guidelines on the use of study results for marketing purposes. These guidelines are described in https://abrf.memberclicks.net/assets/docs/research_group_study_participation_guidelines_2010.pdf

Important Dates

November 27, 2023: Study commences
February 15, 2024: Deadline for results submission
April 21, 2024: Results presentation at the ABRF 2024 Annual Meeting

Questions and Additional Information

Please send questions to [email protected]. Follow this link to obtain a copy of the complete announcement letter for the iPRG-2023 Proteome Informatics Research Group Study on Crosslinking MS Data Analysis.

 Proteomics Cloud Computing Workshops - September - November 2022

The iPRG presented a series of online video tutorials about the use of cloud computing resources for MS-based proteomics, focusing on Nextflow, the Trans-Proteomic Pipeline (TPP) and Galaxy Platform.  Recordings of the tutorials are available on YouTube or they can be accessed directly via this link.

 

Studies

1)    

iPRG 2020 Study on Metaproteomics was launched March 31, 2020. Phase 1 concluded July 31. See original invitation and instructions here. Phase 2 of the Study was completed on January 31, 2021.   
Presentation from the ABRF 2021 Annual Meeting.  Presentation from the ABRF 2022 Annual Meeting.   
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 Study including instructions  
  - Study-related paper in Journal of Proteome Research  
  - Study design and outcome  paper  published in JBT
  - Data deposited in PRIDE
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)
iprg2020_study_instructions_phase_2.pdf

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 Askenazi Dana-Farber Cancer Institute  Member: 03/08 - 03/11
Nuno Bandeira University of California, San Diego  Member: 04/10 - 03/13
Conrad Bessant Cranfield University  Member: 03/09 - 12/09
Christopher Colangelo  Agilent Member: Current
Robert J Chalkley UCSF  Chair: 11/11 - 03/13
Member: 04/10 - 10/11
Hyungwon Choi  National University of Singapore Member: Current
Karl Clauser Broad Institute of MIT and Harvard  Member: 04/09 - 03/12
Darryl L. Davis Janssen Member: Current
Eric Deutsch Institute for Systems Biology  Member: 04/10 - 03/13
Jayson Falkner University of Michigan  Member: 12/07 - 12/09
Melanie Föll University Medical Center Freiburg Member:  Current
Antony Harvey  Protein Metrics Member through 12/22
Michael Hoopmann  Institute for Systems Biology Member: Current
Lukas Käll  Royal Institute of Technology Member: Current
Eugene A. Kapp WEHI  Member: 12/11 - 03/13
Jeffrey A Kowalak NIMH  EB Liaison: 04/07 - 04/10
Henry H. Lam Hong Kong University of Science and Technology  Ad hoc: 12/10 - 03/11
Member: 04/11 - 10/13
William S. Lane Harvard University  Member: 04/07 - 04/10
EB Liaison: 03/06 - 04/07
Lennart Martens Ghent University  Chair: 04/10 - 03/11
Member: 04/08 - 04/10
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
Ben Neely National Institute of Standards and Technology Member through 12/22
Alexey I Nesvizhskii University of Michigan  Member: 03/06 - 03/08
Thomas Neubert New York Univ Sch of Med  EB Liaison: 04/10 - 04/14
Member: 04/14 - 04/17
Magnus Palmblad Leiden University Medical Center

Member: 06/13 - 04/19
Chair:  04/16 - 40/19
EB Liaison:  04/19 - 04/22
Member:  04/22 - present
Samuel Payne  Pacific Northwest National Laboratory Member: Current
Yasset Perez-Riverol  European Bioinformatics Institute Member: Current
Brett S Phinney Proteomics Core UC Davis Genome Center  EB Liaison: 04/14 - 04/15
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: 02/09 - 04/10
Member: 03/06 - 02/08
Sean L. Seymour AB SCIEX  Chair: 03/06 - 02/08
Member: 02/08 - 02/09
David L Tabb Vanderbilt University Medical Center  Member: 03/06 - 02/09

Susan T. Weintraub  

 Univ. of Texas Health Science Center at San Antonio Member: Current

 

Questions or interest in joining an ABRF research group? Contact us!