Journal
NATURE METHODS
Volume 12, Issue 3, Pages 258-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.3255
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Funding
- US National Institutes of Health [5R01GM94231, R01GM107148, U24DK097153]
- Government of Canada through Genome Canada
- Ontario Genomics Institute [OGI-069]
- Canadian Institutes of Health Research [MOP-84314, MOP-123322]
- Singapore Ministry of Education [R-608-000-088-112]
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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.
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