Proteomics,Multiomics

Dataset Information

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

ABSTRACT: This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics", Nature Methods, in press Raw files are deposited here in ProteomeXchange and are associated with the DIA-Umpire processed data. All DIA-Umpire processed results for each sample together with DDA results are deposited in separated folders. Also see the "DataSampleID.xlsx" associated with this Readme file. Internal reference from the Gingras lab ProHits implementation: Project 94, Export version VS2 (Tsou_DIA-Umpire)

OTHER RELATED OMICS DATASETS IN: PXD001587MTBLS417

INSTRUMENT(S): TripleTOF 5600, Q Exactive

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Alexey I. Nesvizhskii  

PROVIDER: MSV000081023 | MassIVE | Thu Apr 27 13:19:00 BST 2017

SECONDARY ACCESSION(S): PXD001587

REPOSITORIES: MassIVE

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

Tsou Chih-Chiang CC   Avtonomov Dmitry D   Larsen Brett B   Tucholska Monika M   Choi Hyungwon H   Gingras Anne-Claude AC   Nesvizhskii Alexey I AI  

Nature methods 20150119 3

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  ...[more]

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