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          Institute: MPI für Entwicklungsbiologie     Collection: Abteilung 1 - Protein Evolution (A. Lupas)     Display Documents



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ID: 733228.0, MPI für Entwicklungsbiologie / Abteilung 1 - Protein Evolution (A. Lupas)
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets
Authors:Griss, J.; Perez-Riverol, Y.; Lewis, S.; Tabb, D. L.; Dianes, J. A.; Del-Toro, N.; Rurik, M.; Walzer, M. W.; Kohlbacher, O.; Hermjakob, H.; Wang, R.; Vizcaino, J. A.
Date of Publication (YYYY-MM-DD):2016-08
Title of Journal:Nat Methods
Volume:13
Issue / Number:8
Start Page:651
End Page:656
Review Status:Internal review
Audience:Not Specified
Abstract / Description:Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra.
External Publication Status:published
Document Type:Article
Affiliations:MPI für Entwicklungsbiologie/Abteilung 1 - Proteinevolution (Andrei Lupas)
External Affiliations:European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville. Dept. of Computer Science, University of Tubingen, Germany; Center for Bioinformatics, University of Tubingen, Germany. Dept. of Computer Science, University of Tubingen, Germany; Center for Bioinformatics, University of Tubingen, Germany; Quantitative Biology Center, University of Tubingen, Germany; Max Planck Institute for Developmental Biology, Germany. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom; National Center for Protein Sciences, Beijing, China.
Identifiers:ISSN:1548-7105 (Electronic) 1548-7091 (Linking) %R 10.1... [ID No:1]
URL:https://www.ncbi.nlm.nih.gov/pubmed/27493588 [ID No:2]
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