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: MTBLS417MSV000081023

INSTRUMENT(S): TripleTOF 5600, Q Exactive

ORGANISM(S): Homo Sapiens (human) Escherichia Coli

TISSUE(S): Cell Culture

SUBMITTER: Chih-Chiang Tsou  

LAB HEAD: Alexey I. Nesvizhskii

PROVIDER: PXD001587 | Pride | 2015-01-21

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
140120_Lysate90min_38.mzXML Mzxml
140120_Lysate90min_38.raw Raw
140120_Lysate_90min_DIA_53.mzXML Mzxml
140120_Lysate_90min_DIA_53.raw Raw
18185_REP2_4pmol_UPS2_IDA_1.mzXML Mzxml
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Publications

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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