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.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Tsou CC,Avtonomov D,Larsen B,Tucholska M,Choi H,Gingras AC,Nesvizhskii AIdoi
10.1038/nmeth.3255subject
Has Abstractpub_date
2015-03-01 00:00:00pages
258-64, 7 p following 264issue
3eissn
1548-7091issn
1548-7105pii
nmeth.3255journal_volume
12pub_type
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