PXD001587

PXD001587 is an original dataset announced via ProteomeXchange.

Title	DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics
Description	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)
HostingRepository	PRIDE
AnnounceDate	2015-01-21
AnnouncementXML	Submission_2015-01-21_08:44:43.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chih-Chiang Tsou
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive; TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2014-12-09 01:50:26	ID requested
⏵ 1	2015-01-21 08:44:44	announced

Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI, DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods, 12(3):258-64, 7 p following 264(2015) [pubmed]

submitter keyword: DIA, SWATH

Alexey I. Nesvizhskii
contact affiliation	University of Michigan
contact email	nesvi@umich.edu
lab head
Chih-Chiang Tsou
contact affiliation	University of Michigan
contact email	tsouc@umich.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/01/PXD001587

PRIDE project URI

• PRIDE
  1. PXD001587
     1. Label: PRIDE project
     2. Name: DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics