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PXD026600 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleExtensive and accurate benchmarking of DIA acquisition methods and softwares using a complex
DescriptionIn 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).
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterArnaud Droit
SpeciesList scientific name: Escherichia coli; common name: E. coli; NCBI TaxID: 562; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListOxidation; Carbamidomethyl
InstrumentOrbitrap Fusion ETD
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-06-09 11:33:32ID requested
12021-09-16 10:15:25announced
Publication List
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]
Keyword List
submitter keyword: DIA workflow, benchmark, quantitication, proteomic standard
Contact List
Arnaud Droit
contact affiliationCHU de Quebec Universite Laval
contact emailarnaud.droit@crchuq.ulaval.ca
lab head
Arnaud Droit
contact affiliationCHU de Quebec Universite Laval
contact emailarnaud.droit@crchuq.ulaval.ca
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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