PXD026600-1

PXD026600 is an original dataset announced via ProteomeXchange.

Title	Extensive and accurate benchmarking of DIA acquisition methods and softwares using a complex
Description	In order to compare workflows for acquisition and treatment of proteomic data analyzed in Data Independent Acquisition (DIA) mode, a proteomic standard has been generated by spike-in the 48 human proteins of UPS1 (Sigma) in a whole cell extract of E.coli at 8 different concentrations ranging from 0.1 to 50 fmol of UPS1/ug of E.coli. Each sample has been trypsin-digested analyzed in triplicate on an Orbitrap Fusion instrument (Thermo) operating in DIA mode with four different sizes of precursor windows (narrow, wide, mixed or overlapped). These 4 x 24 raw files have then been analyzed with 6 different DIA softwares (Spectronaut, ScaffoldDIA, Skyline, DIA-Umpire, OpenSWATH and DIA-NN) with the use or not of a fractionated E.coli library. Here we deposit: the 96 Thermo raw files of the analysis as well as the corresponding converted .mzML and mzXML files; the 49 DDA .raw files for the spectral library, composed of the 48 fractions of E.coli whole cell extract + 200 fmol/ug of UPS1 proteins; the spectral library generated by the DDA analysis (.blib and .tsv files generated with Skyline, .tsv file from Spectronaut); the spectral library generated with the fasta file in Prosit; the spectral library generated by the 24 Narrow DIA analysis and the fasta file in DIA-NN and MSFragger (DIA-Umpire SE module); the Fasta file; the software tool files (Spectronaut .sne files, Skyline .sky files and ScaffoldDIA .sdia files); the raw outputs of the tools and the post-processed precursors quantification tables (normalized, imputed missing values), for the 4 acquisition modes (5 with the use of a peptide library and 4 with a search against Human + E.coli fasta files).
HostingRepository	MassIVE
AnnounceDate	2021-09-16
AnnouncementXML	Submission_2021-09-16_10:15:25.064.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Arnaud Droit
SpeciesList	scientific name: Escherichia coli; common name: E. coli; NCBI TaxID: 562; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-09 11:33:32	ID requested
⏵ 1	2021-09-16 10:15:25	announced

Gotti C, Roux-Dalvai F, Joly-Beauparlant C, Mangnier L, Leclercq M, Droit A, Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard. J Proteome Res, 20(10):4801-4814(2021) [pubmed]

submitter keyword: DIA workflow, benchmark, quantitication, proteomic standard

Arnaud Droit
contact affiliation	CHU de Quebec Universite Laval
contact email	arnaud.droit@crchuq.ulaval.ca
lab head
Arnaud Droit
contact affiliation	CHU de Quebec Universite Laval
contact email	arnaud.droit@crchuq.ulaval.ca
dataset submitter

MassIVE dataset URI

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://massive.ucsd.edu/MSV000087597/