Center for Computational Mass Spectrometry

Projects, Collaborations, and Community

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Collaborate With Us!

We are often approached with collaborative proposals that either require new algorithmic and software developments or a new creative use of existing tools. In the last 5 years, CCMS have been collaborating with over 50 laboratories and published nearly 70 papers resulting from these collaborations. Please do not hesitate to email ccms@ucsd.edu or to write directly to Drs. Bafna, Bandeira, and Pevzner if you have ideas for new collaborations. Your proposal should outline the scientific focus, how the proposed collaboration would work, its scope, and how the proposed research would draw upon the unique capabilities of CCMS.

In addition to driving technology development in the P41 BTRC, the review criteria for new projects includes an evaluation of its scientific excellence, applicability to biomedical research, innovation, suitability for the Resource, and a likelihood of meeting successful benchmarks. Please note that no financial support will be provided by CCMS to the collaborator; the intent is that CCMS will fully cover the research costs for the development of computational aspects of the proposed collaboration.

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Projects, Collaborations and Community

Driving Biological Projects

From Monoclonal to Polyclonal Antibody Sequencing
Primary Collaborator(s): Jennie Lill
Collaborator(s) Institution: Dept. of Protein Chemistry, Genentech
CCMS Personnel: Vineet Bafna, Nuno Bandeira, Pavel Pevzner
A Systems Approach towards the Therapeutic Modulation of the Acetylome
Primary Collaborator(s): Anne-Claude Gingras
Collaborator(s) Institution: Samuel Lunenfeld Institute
CCMS Personnel: Vineet Bafna, Nuno Bandeira, Pavel Pevzner
Interspecies chemical interactions
Primary Collaborator(s): Kit Pogliano, Pieter Dorrestein
Collaborator(s) Institution: Division of Biological Sciences at UCSD, School of Pharmacy at UCSD
CCMS Personnel: Nuno Bandeira, Pavel Pevzner
Proteogenomic Development of Breast Cancer Vaccines
Primary Collaborator(s): Paul Spellman (Oregon Health Sciences University), Peter Lee (City of Hope Hospital), Jill Slansky (University of Colorado)
CCMS Personnel: Vineet Bafna, Nuno Bandeira
Proteogenomics approach to studies of polybacterial infections
Primary Collaborator(s): Jeffrey McLean
Collaborator(s) Institution: J. Craig Venter Institute
CCMS Personnel: Pavel Pevzner
Protein-Protein Interactions and PTMs in Cataractous Lens
Primary Collaborator(s): Larry David
Collaborator(s) Institution: Oregon Health and Sciences University
CCMS Personnel: Vineet Bafna, Nuno Bandeira, Pavel Pevzner
Proteomic Biomarkers for Drug Toxicity in Cancer Patients
Primary Collaborator(s): Emily Chen, Dawn Hershman
Collaborator(s) Institution: Columbia University Mecial Center
CCMS Personnel: Vineet Bafna, Nuno Bandeira, Pavel Pevzner
Discovery of Lantibiotics
Primary Collaborator(s): Willem (Wilfred) van der Donk
Collaborator(s) Institution: Department of Chemistry, University of Illinois at Urbana-Champaign, Howard Hughes Medical Institute
CCMS Personnel: Nuno Bandeira, Pavel Pevzner
Clinical Cancer Proteogenomics
Primary Collaborator(s): Richard Smith, Karin Rodland, Sam Payne
Collaborator(s) Institution: PNNL
CCMS Personnel: Vineet Bafna
Unraveling the Combinatorial Histone Code in Human Diseases
Primary Collaborator(s): Benjamin Garcia
Collaborator(s) Institution: Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania
CCMS Personnel: Vineet Bafna, Pavel Pevzner

projects, Collaborations, and Community

Accomplished Collaborations & Service Projects

Primary Collaborator(s): Richard Smith (PNNL)
Collaborator(s) Institution: PNNL
CCMS Personnel: Pavel Pevzner, Nuno Bandeira, Ari Frank
Project Dates: 2008-2012
Publications: Clustering millions of tandem mass spectra.
Primary Collaborator(s): Eunok Paek (University of Seoul)
Collaborator(s) Institution: University of Seoul
CCMS Personnel: Nuno Bandeira, Seujin Na
Project Dates: 2000-2012
Publications: Fast multi-blind modification search through tandem mass spectrometry
Publications:
Primary Collaborator(s): Bill Gerwik (UCSD)
Collaborator(s) Institution: UCSD
CCMS Personnel: Pavel Pevzner, Pieter Dorrestein, Hosein Mohimani
Project Dates: 2009-2010
Publications: Synergistic allelochemicals from a freshwater cyanobacterium
Primary Collaborator(s): Neil Kelleher (UIUC)
Collaborator(s) Institution: UIUC
CCMS Personnel: Pavel Pevzner, Ari Frank
Project Dates: 2008-2009
Publications: Interpreting top-down mass spectra using spectral alignment.
Primary Collaborator(s): Jeff Smith (Burnham), Andrei Osterman (Burnham).
Collaborator(s) Institution: Burnham
CCMS Personnel: Pavel Pevzner, Nitin Gupta
Project Dates: 2010-2012
Primary Collaborator(s): Richard Smith (PNNL)
Collaborator(s) Institution: PNNL
CCMS Personnel: Pavel Pevzner, Nitin Gupta, Jesse Rodriguez
Project Dates: July 2010- 2012
Publications: Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry.
Publications: Does trypsin cut before proline?
Publications:
Primary Collaborator(s): Javier Satulovsky (Agilent Technologies), Roman Zubarev (Karolinska Institute).
Collaborator(s) Institution: Agilent Technologies
CCMS Personnel: Pavel Pevzner, Sangtae Kim, Ilya Kolykhmatov
Project Dates: 2009-2011
Primary Collaborator(s): Matthias Mann (MPI)
Collaborator(s) Institution: MPI
CCMS Personnel: Nuno Bandeira, Pavel Pevzner
Project Dates: 2008-2009
Publications: Multi-spectra peptide sequencing and its applications to multistage mass spectrometry
Publications:
Primary Collaborator(s): Parag Mallick (Stanford).
Collaborator(s) Institution: Stanford
CCMS Personnel: Nuno Bandeira, Jian Wang
Project Dates: 2009-2010
Publications: Peptide identification from mixture tandem mass spectra.
Publications: Peptide identification by database search of mixture tandem mass spectra.
Publications:
Primary Collaborator(s): Eduardo Macagno (UCSD), Pieter Dorrestein (UCSD), Terry Gaasterland (UCSD), Isabelle Fournier (Universit de Lille)
Collaborator(s) Institution: UCSD
CCMS Personnel: Vineet Bafna, Jocelyne Bruand
Project Dates: 2008-2012
Publications: Automated querying and identification of novel peptides using MALDI mass spectrometric imaging
Publications:
Primary Collaborator(s): Eduardo Macagno (UCSD), Theodore Alexandrov (University of Bremen), Michel Salzet (Universite de Lille), Isabelle Fournier (Universite de Lille).
Collaborator(s) Institution: UCSD
CCMS Personnel: Vineet Bafna, Jocelyne Bruand
Project Dates: 2008-2012
Publications: AMASS: algorithm for MSI analysis by semi-supervised segmentation
Publications:
Primary Collaborator(s): Eduardo Macagno (UCSD), Michel Salzet (Universite de Lille), Isabelle Fournier (Universite de Lille)
Collaborator(s) Institution: UCSD
CCMS Personnel: Vineet Bafna, Nuno Bandeira, Jocelyne Bruand
Project Dates: 2008-2012
Primary Collaborator(s): Julia Laskin (PNNL).
Collaborator(s) Institution: PNNL
CCMS Personnel: Vineet Bafna, Jocelyne Bruand, Doruk Beyter
Project Dates: 2008-2012
Publications:
Primary Collaborator(s): Michael MacCoss (U. Washington), Bill Noble (U. Washington), Uri Keich (University Of Sydney), Lukas Kall (University of Stockholm)
Collaborator(s) Institution: U. Washington
CCMS Personnel: Nuno Bandeira,Pavel Pevzner, Nitin Gupta
Project Dates: 2010-2012
Publications: Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing
Publications:
Elucidating novel proteolytic mechanisms for producing neuropeptides
Primary Collaborator(s): Vivian Hook (UCSD).
Collaborator(s) Institution: UCSD
CCMS Personnel: Pavel Pevzner, Nitin Gupta
Project Dates: 2010-2011
Publications: Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing
Publications:
Peptide identification from ETD/CID pairs
Primary Collaborator(s): Albert Heck (University of Utrecht), Magnus Palmblad (Leiden University)
Collaborator(s) Institution: University of Utrecht
CCMS Personnel: Nuno Bandeira, Pavel Pevzner, Sangtae Kim
Project Dates: Sep 2011-Dec 2012
Publications: The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search
Publications:
Correlating Leech Proteogenomics with MS Imaging
Primary Collaborator(s): Terry Gaasterland (UCSD), Eduardo Macagno (UCSD)
Collaborator(s) Institution: UCSD
CCMS Personnel: Vineet Bafna, Jocelyne Bruand, Sunghee Woo
Project Dates: 2008-2012
Sequencing Cyclic Peptides by Multistage Mass Spectrometry
Primary Collaborator(s): Pieter Dorrestein (UCSD)
Collaborator(s) Institution: UCSD
CCMS Personnel: Pavel Pevzner, Hosein Mohimani
Project Dates: 2011-2012
Publications: Sequencing cyclic peptides by multistage mass spectrometry.
Publications:
Detecting Phosphopantetheinyl modified Peptides
Primary Collaborator(s): Jordan Meier (CalTech), Michael Burkart (UCSD).
Collaborator(s) Institution: CalTech, UCSD
CCMS Personnel: Vineet Bafna, Pieter Dorrestein, Anand Patel
Project Dates: 2008-2010
Publications: Practical 4'-phosphopantetheine active site discovery from proteomic samples.
Publications:
http://www.ncbi.nlm.nih.gov/pubmed/22414154
Primary Collaborator(s): William Fenical (UCSD).
Collaborator(s) Institution: UCSD
CCMS Personnel: Pavel Pevzner, Pieter Dorrestein, Hosein Mohimani
Project Dates: Oct. 2011 – June, 2013
Publications: Multiplex de novo sequencing of peptide antibiotics.
Publications:
Protein Quantification using Shared Peptides
Primary Collaborator(s): Steve Briggs (UCSD)
Collaborator(s) Institution: UCSD
CCMS Personnel: Nuno Bandeira, Vineet Bafna, Banu Dost
Project Dates: 2008- 2009
Publications: Accurate mass spectrometry based protein quantification via shared peptides.
Publications:
Cycloquest - database search for cyclic peptides
Primary Collaborator(s): Michelle Colgrave (CSIRO Livestock Industries) and Michael Selsted (USC)
Collaborator(s) Institution: CSIRO Livestock Industries, USC
CCMS Personnel: Pavel Pevzner, Hosein Mohimani, Stefano Bonissone
Project Dates: 2010- June, 2012
Publications: Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases.
Publications:
Cycloquest - database search for cyclic peptides
Primary Collaborator(s): Michelle Colgrave (CSIRO Livestock Industries) and Michael Selsted (USC)
Collaborator(s) Institution: CSIRO Livestock Industries, USC
CCMS Personnel: Pavel Pevzner, Hosein Mohimani, Stefano Bonissone
Project Dates: 2010- June, 2012
Publications: Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases.
Publications:
Cycloquest - database search for cyclic peptides
Primary Collaborator(s): Michelle Colgrave (CSIRO Livestock Industries) and Michael Selsted (USC)
Collaborator(s) Institution: CSIRO Livestock Industries, USC
CCMS Personnel: Pavel Pevzner, Hosein Mohimani, Stefano Bonissone
Project Dates: 2010- June, 2012
Publications: Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases.
Publications:
iPRG 2011: Identification of Electron Transfer Dissociation (ETD) Mass Spectra
Primary Collaborator(s): ABRF Proteome Informatics Research Group (iPRG)
Collaborator(s) Institution: ABRF Proteome Informatics Research Group (iPRG)
CCMS Personnel: Nuno Bandeira
Project Dates: Oct 2010 - Feb 2011
iPRG 2012: A Study on Detecting Modified Peptides in a Complex Mixture
Primary Collaborator(s): ABRF Proteome Informatics Research Group (iPRG)
Collaborator(s) Institution: ABRF Proteome Informatics Research Group (iPRG)
CCMS Personnel: Nuno Bandeira
Project Dates: Oct 2011 - Feb 2012
Publications: Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.
Publications:
iPRG 2013: Using RNA-Seq Data to Refine Proteomic Data Analysis
Primary Collaborator(s): ABRF Proteome Informatics Research Group (iPRG)
Collaborator(s) Institution: ABRF Proteome Informatics Research Group (iPRG)
CCMS Personnel: Nuno Bandeira
Project Dates: Oct 2012 - Feb 2013
Jan 2012- June 2012
Primary Collaborator(s): Joshua Coon, University of Wisconsin
Collaborator(s) Institution: University of Wisconsin
CCMS Personnel: Nuno Bandeira, Adrian Guthals
Project Dates: Aug 2013 - Dec 2013
Publications: Neutron-encoded signatures enable product ion annotation from tandem mass spectra.
Publications:
Open data formats for proteomics: mzIdentML support in MS-GF
Primary Collaborator(s): Andrew Jones, University of Liverpool, UK
Collaborator(s) Institution: University of Liverpool, UK
CCMS Personnel: Nuno Bandeira, Sangtae Kim
Project Dates: Jan 2012- June 2012
CPTAC integration of MS-GF and False Localization Rates
Primary Collaborator(s): Paul Rudnick, NIST
Collaborator(s) Institution: NIST
CCMS Personnel: Nuno Bandeira, Sangtae Kim, June Snedecor
Project Dates: Jan 2013- July 2013
False localization rates for PTM site assignments
Primary Collaborator(s): Huilin Zhou (UCSD)
Collaborator(s) Institution: UCSD
CCMS Personnel: Vineet Bafna, Nuno Bandeira, June Snedecor
Project Dates: 2010-Current
Generating peptide sequence tags for top-down spectra
Primary Collaborator(s): Kira Vyatkina (St. Petersburg Academic University), Lijiljana Pasa-Tolic (PNNL)
Collaborator(s) Institution: St. Petersburg Academic University, PNNL
CCMS Personnel: Pavel Pevzner, Xiaowen Liu, Stefano Bonissone
Project Dates: 2012-Current
Optimizing antibody proteogenomics pipeline at Genentech.
Primary Collaborator(s): Jennie Lill (Genentech)
CCMS Personnel: Nuno Bandeira, Vineet Bafna, Adrian Guthals, Natalie Castellana, Stefano Bonissone
Project Dates: 2007 - Current
Publications: PMID:20164058
Publications: PMID:21268269
New approach for identification of SUMOylated peptides.
Primary Collaborator(s): Jennie Lill (Genentech)
CCMS Personnel: Nuno Bandeira, Jian Wang
Project Dates: Aug 2012 - Current
Publications: PMID:24437954
Combining MS and NGS for analyzing brain proteome.
Primary Collaborator(s): Philip Khaitovich (Max Planck Institute, Shanghai)
CCMS Personnel: Pavel Pevzner, Boyko Kakaradov, Stefano Bonissone
Project Dates: 2011 - Current
Discovery and phasing of SNPs using bottom-up and top-down MS.
Primary Collaborator(s): David Herold (VA Hospital, San Diego)
CCMS Personnel: Nuno Bandeira, June Snedecor
Project Dates: 2012 – Current
High throughput identification of top-down spectra.
Primary Collaborator(s): Julian Whitelegge (UCLA), David R. Goodlett (University of Washington), Richard D. Smith (PNNL), Lijiljana Pasa-Tolic(PNNL)
CCMS Personnel: Vineet Bafna, Pavel Pevzner, Xiaowen Liu, Stefano Bonissone
Project Dates: Aug 2010 - Current
Publications: PMID:22027200
Publications: PMID:24188097
Publications: PMID:23720318
Publications: PMID:20855543
Improving signal peptide prediction via mass spectrometry.
Primary Collaborator(s): Dmitry Frishman (Technical University of Munich), Sam Payne (PNNL)
CCMS Personnel: Pavel Pevzner, Stefano Bonissone
Project Dates: Sep 2011 - Current
Publications: PMID:23556536
Learning functions of NRP and RiPP biosynthetic enzymes by MS.
Primary Collaborator(s): Marnix Medama (University of Groningen)
CCMS Personnel: Pavel Pevzner, Pieter Dorrestein, Hosein Mohimani
Project Dates: Jan 2013 - Current
Natural product discovery by MS and genome mining.
Primary Collaborator(s): Pieter Dorrestein (UCSD), Wilfred van der Donk (UIUC)
CCMS Personnel: Pavel Pevzner, Hosein Mohimani, Stefano Bonissone
Project Dates: June 2012 - Current
Publications: Submitted
Dereplication and sequencing of marine non-ribosomal peptides.
Primary Collaborator(s): Pieter Dorrestein (UCSD), William Gerwick (UCSD) and Roger Linington (UCSC)
CCMS Personnel: Nuno Bandeira, Pavel Pevzner, Julio Ng, Hosein Mohimani, Stefano Bonissone
Project Dates: 2009 - Current
Publications: PMID:19413302
Publications: PMID:19597502
Publications: PMID:20534563
Publications: PMID:20805502
Assessing spectrum-spectrum match significance for neuropeptidomics.
Primary Collaborator(s): Pieter Dorrestein (UCSD), Vivian Hook (UCSD)
CCMS Personnel: Nuno Bandeira, Mingxun Wang
Project Dates: Jan 201 - Current
Publications: PMID:23808827
De novo protein sequencing of snake venoms and antibodies.
Primary Collaborator(s): Karl Clauser (Broad Institute), Jennie Lill (Genentech), David Goodlett (U Washington), Toni Koller (SUNY Stony Brook), Olga Haim (Universidade Federal do Parana, Brazil), Richard Valente (Foundation Oswaldo Cruz, Brazil), Kira Vyatkina (Saint Petersburg Academic University), Ljijljana Pasa-Tolic (PNNL)
CCMS Personnel: Nuno Bandeira, Vineet Bafna, Pavel Pevzner, Natalie Castellana, Xiaowen Liu, Adrian Guthals, Joao Canhita
Project Dates: 2008 – Current
Publications: PMID:18785330
Publications: PMID:19060866
Publications: PMID:22798278
Publications: PMID:23679345
Publications: PMID:17446555
Optimizing proteogenomics annotation pipeline for very large spectral datasets.
Primary Collaborator(s): Steve Briggs (UCSD), Laurie Smith (UCSD)
CCMS Personnel: Vineet Bafna, Natalie Castellana, Sunghee Woo
Project Dates: Aug 2008 - Current
Publications: PMID:20620248
Publications: PMID:19098097
Publications: PMID:24248366
Mismatch-tolerant spectral library searches.
Primary Collaborator(s): Emily Chen (Columbia University), Toni Koller (SUNY Stony Brooks)
CCMS Personnel: Nuno Bandeira, Mingxun Wang
Project Dates: Jan 2012 - Current
N-terminal protein processing and N-acetylation.
Primary Collaborator(s): Ralph Bradshaw (UCSF), Margie Romine (PNNL)
CCMS Personnel: Pavel A. Pevzner, Stefano Bonissone
Project Dates: May 2012 - current
Publications: PMID:23001859
Identification of protein-protein interaction using cross-linking.
Primary Collaborator(s): Phil Andrews (U. Michigan)
Collaborator(s) Institution: U. Michigan
CCMS Personnel: Nuno Bandeira, Jian Wang
Project Dates: Aug 2012 – Current
Development of Enosi proteogenomics tool and its integration with EMC storage solutions.
Primary Collaborator(s): Kamil Isaev (EMC)
Collaborator(s) Institution: EMC
CCMS Personnel: Pavel Pevzner, Vineet Bafna, Nuno Bandeira
Project Dates: Sep 2013 - Current
De novo sequencing of unyielding monoclonal antibodies.
Primary Collaborator(s): Michael MacCoss (University of Washington)
Collaborator(s) Institution: University of Washington
CCMS Personnel: Nuno Bandeira, Adrian Guthals
Project Dates: Jan 2013 - Current
Open data formats for proteomics: mzTab format.
Primary Collaborator(s): Juan Vizcaino (European Bioinformatics Institute, UK)
Collaborator(s) Institution: European Bioinformatics Institute, UK
CCMS Personnel: Nuno Bandeira
Project Dates: 2012 - Current
Publications: Submitted
Search for bioactive endogenous peptides using spectral networks.
Primary Collaborator(s): Michael Djordjevic (Australian National University, Canberra, Australia)
Collaborator(s) Institution: Australian National University, Canberra, Australia
CCMS Personnel: Nuno Bandeira, Ming Wang
Project Dates: July 2013 - Current
Cancer proteogenomics.
Primary Collaborator(s): Shiv Nagaraj (Univ. Queensland, Australia)
Collaborator(s) Institution: Univ. Queensland, Australia
CCMS Personnel: Vineet Bafna, Seong Cha
Project Dates: Aug 2012 - Current
MassIVE integration with ProteomeXchange.
Primary Collaborator(s): Henning Hermjakob (European Bioinformatics Institute, UK)
Collaborator(s) Institution: European Bioinformatics Institute, UK
CCMS Personnel: Nuno Bandeira, Jeremy Carver
Project Dates: Aug 2012 - Current
Publications: (Nature Biotech, in press)
C. elegans proteogenomics.
Primary Collaborator(s): Michael MacCoss (University of Washington)
Collaborator(s) Institution: University of Washington
CCMS Personnel: Vineet Bafna, Sunghee Woo
Project Dates: Dec 2012- Current
Publications: PMID:23802565
Constructing the mass-spectrometry encyclopedia of neurotransmitters.
Primary Collaborator(s): Vivian Hook (UCSD)
CCMS Personnel: Nuno Bandeira, Pavel Pevzner, Jian Wang, Yoona Kim
Project Dates: 2009 – Current
Publications: PMID:21821666
Publications: PMID:20734175
Publications: PMID:20704348
Identification of cross-links using top-down mass spectrometry.
Primary Collaborator(s): Ljiljana Pasa-Tolic (PNNL)
CCMS Personnel: Pavel Pevzner, Vineet Bafna, Xiaowen Liu, Stefano Bonissone
Project Dates: Jan 2011- Current
Antibiotics discovery using genome mining in fragmented bacterial datasets.
Primary Collaborator(s): Bill Gerwick (UCSD), Lixin Zhang (Institute for Microbiology, Beijing, China)
CCMS Personnel: Pavel Pevzner, Dmitry Brinza, Hosein Mohimani
Project Dates: Jan. 2010- Current
Publications: PMID:21533272
Publications: PMID:21488639
Publications: PMID:20534563
Integration of CCMS Proteogenomics tools in the Galaxy-P and BaseSpace platforms.
Primary Collaborator(s): Anne-Francois Lamblin (University of Minnesota), Ilya Chorny (Illumina)
CCMS Personnel: Vineet Bafna, Sunghee Woo
Project Dates: Dec 2013- Current
Identification of novel gene structures in model organisms.
Primary Collaborator(s): Akhilesh Pandey
Collaborator(s) Institution: Johns Hopkins University
CCMS Personnel: Vineet Bafna, Sunghee Woo
Project Dates: Aug 2012- Current
Peptide fragmentation models for new enzymes
Primary Collaborator(s): Elizabeth Komives
Collaborator(s) Institution: UCSD
CCMS Personnel: Nuno Bandeira, Pavel Pevzner, Sangtae Kim, Adrian Guthals
Publications: PMID: 24425750
Spectral archives: a novel approach to analyzing tandem mass spectra
Primary Collaborator(s): R. Smith (PNNL).
Collaborator(s) Institution: PNNL
CCMS Personnel: Pavel Pevzner, Ari Frank, Ilya Kolykhmatov
Project Dates: 2011-Current
Publications: Clustering millions of tandem mass spectra.
Publications: Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.
Publications:
Finding unusual signal peptides
Primary Collaborator(s): Sam Payne (PNNL)
Collaborator(s) Institution: PNNL
CCMS Personnel: Pavel Pevzner, Stefano Bonissone
Project Dates: 2012-Current
Publications: Unexpected diversity of signal peptides in prokaryotes.
Publications:
De novo protein sequencing using top-down MS
Primary Collaborator(s): Ljiljana Pasa-Tolic (PNNL); Kira Vyatkina (St. Petersburg Academic University), Leonard Dekker (Erasmus Medical Center)
Collaborator(s) Institution: PNNL, St. Petersburg Academic University, Erasmus Medical Center
CCMS Personnel: Vineet Bafna, Pavel Pevzner, Xiaowen Liu, Stefano Bonissone
Project Dates: 2013-Current
Publications: submitted
Open data formats for proteomics data: mzIdentML support in MS-GF+
Primary Collaborator(s): Andrew Jones
Collaborator(s) Institution: University of Liverpool, UK
CCMS Personnel: Santae Kim
Project Dates: 2012
iPRG 2013: Using RNA-Seq Data to Refine Proteomic Data Analysis
Collaborator(s) Institution: ABRF Proteome Informatics Research Group (iPRG)
CCMS Personnel: Nuno Bandeira
Project Dates: Oct 2012 - Feb 2013
Publications: Study Results
iPRG 2012: A Study on Detecting Modified Peptides in a Complex Mixture
Collaborator(s) Institution: ABRF Proteome Informatics Research Group (iPRG)
CCMS Personnel: Nuno Bandeira
Project Dates: Oct 2011 - Feb 2012
Publications: PMID: 24187338
Publications: Study Results
iPRG 2011: Identification of Electron Transfer Dissociation (ETD) Mass Spectra
Collaborator(s) Institution: ABRF Proteome Informatics Research Group (iPRG)
CCMS Personnel: Nuno Bandeira
Project Dates: Oct 2010 - Feb 2011
Publications: Study Results
Scoring models and de novo sequencing for neutron-encoded MS
Primary Collaborator(s): Joshua Coon
Collaborator(s) Institution: University of Wisconsin
CCMS Personnel: Nuno Bandeira, Adiean Guthals
Project Dates: Aug 2013 - Dec 2013
Publications: PMID: 24043425
Funding: NIGMS GM080148, NHGRI 5T32HG002760, NLM T15LM007359, NSF/NIH T32GM008505
MS-GF+ scoring models for new enzymes
Primary Collaborator(s): Elizabeth Komives
Collaborator(s) Institution: UCSD
CCMS Personnel: Nuno Bandeira, Sangtae Kim, Adrian Guthals