Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

被引：127

作者：

Griss, Johannes ^{[1
,2
]}

Perez-Riverol, Yasset ^{[2
]}

Lewis, Steve ^{[2
]}

Tabb, David L. ^{[3
]}

Dianes, Jose A. ^{[2
]}

del-Toro, Noemi ^{[2
]}

Rurik, Marc ^{[4
,5
]}

Walzer, Mathias ^{[4
,5
]}

Kohlbacher, Oliver ^{[4
,5
,6
,7
]}

Hermjakob, Henning ^{[2
,8
]}

Wang, Rui ^{[2
]}

Vizcaino, Juan Antonio ^{[2
]}

机构：

[1] Med Univ Vienna, Div Immunol Allergy & Infect Dis, Dept Dermatol, Vienna, Austria

[2] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge, England

[3] Vanderbilt Univ, Sch Med, Dept Biomed Informat, Nashville, TN 37212 USA

[4] Univ Tubingen, Dept Comp Sci, Tubingen, Germany

[5] Univ Tubingen, Ctr Bioinformat, Tubingen, Germany

[6] Univ Tubingen, Quantitat Biol Ctr, Tubingen, Germany

[7] Max Planck Inst Dev Biol, Tubingen, Germany

[8] Natl Ctr Prot Sci, Beijing, Peoples R China

来源：

NATURE METHODS | 2016年 / 13卷 / 08期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

TANDEM MASS-SPECTRA; PROTEIN IDENTIFICATION; PEPTIDE IDENTIFICATION; PRIDE DATABASE; DATA SET; SPECTROMETRY; CELLS; PHOSPHOPROTEOME; PROTEOMEXCHANGE; CHROMATOGRAPHY;

D O I：

10.1038/NMETH.3902

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average, 75% of spectra analyzed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large scale to shed light on these unidentified spectra. The Proteomics Identifications (PRIDE) Database Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in the PRIDE Archive, coming from hundreds of data sets, we were able to consistently characterize spectra into three distinct groups: (1) incorrectly identified, (2) correctly identified but below the set scoring threshold, and (3) truly unidentified. Using multiple complementary analysis approaches, we were able to identify similar to 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.

引用

页码：651 / +

页数：8

共 40 条

[1] Mass spectrometry-based proteomics [J].