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).
[doi:10.25345/C57C0G]
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: DIA workflow ; benchmark ; quantitication ; proteomic standard
Principal Investigators: (in alphabetical order) |
Arnaud Droit, CHU de Quebec Universite Laval, Canada |
Submitting User: | Arno |
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. Epub 2021 09 02.
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Identification Results | ||
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Quantification Results | ||
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Browse Quantification Results | |
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