DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.

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TitleDIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.
Publication TypeJournal Article
Year of Publication2015
AuthorsTsou C-C, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras A-C, Nesvizhskii AI
JournalNat Methods
Volume12
Issue3
Pagination258-64, 7 p following 264
Date Published2015 Mar
ISSN1548-7105
KeywordsAlgorithms, Databases, Protein, Humans, Mass Spectrometry, Metabolomics, Peptide Fragments, Proteins, Proteomics, Software, Workflow
Abstract

As a result of recent improvements in mass spectrometry (MS), there is increased interest in data-independent acquisition (DIA) strategies in which all peptides are systematically fragmented using wide mass-isolation windows ('multiplex fragmentation'). DIA-Umpire (http://diaumpire.sourceforge.net/), a comprehensive computational workflow and open-source software for DIA data, detects precursor and fragment chromatographic features and assembles them into pseudo-tandem MS spectra. These spectra can be identified with conventional database-searching and protein-inference tools, allowing sensitive, untargeted analysis of DIA data without the need for a spectral library. Quantification is done with both precursor- and fragment-ion intensities. Furthermore, DIA-Umpire enables targeted extraction of quantitative information based on peptides initially identified in only a subset of the samples, resulting in more consistent quantification across multiple samples. We demonstrated the performance of the method with control samples of varying complexity and publicly available glycoproteomics and affinity purification-MS data.

DOI10.1038/nmeth.3255
Alternate JournalNat. Methods
PubMed ID25599550
PubMed Central IDPMC4399776
Grant List5R01GM94231 / GM / NIGMS NIH HHS / United States
MOP-123322 / / Canadian Institutes of Health Research / Canada
MOP-84314 / / Canadian Institutes of Health Research / Canada
R01 GM094231 / GM / NIGMS NIH HHS / United States
R01GM107148 / GM / NIGMS NIH HHS / United States
U24 DK097153 / DK / NIDDK NIH HHS / United States
U24DK097153 / DK / NIDDK NIH HHS / United States