Proteomics

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Extensive and accurate benchmarking of DIA acquisition methods and softwares using a complex


ABSTRACT: 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).

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Arnaud Droit  

PROVIDER: MSV000087597 | MassIVE | Wed Jun 09 11:33:00 BST 2021

SECONDARY ACCESSION(S): PXD026600

REPOSITORIES: MassIVE

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Publications

Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard.

Gotti Clarisse C   Roux-Dalvai Florence F   Joly-Beauparlant Charles C   Mangnier Loïc L   Leclercq Mickaël M   Droit Arnaud A  

Journal of proteome research 20210902 10


Over the past decade, the data-independent acquisition mode has gained popularity for broad coverage of complex proteomes by LC-MS/MS and quantification of low-abundance proteins. However, there is no consensus in the literature on the best data acquisition parameters and processing tools to use for this specific application. Here, we present the most comprehensive comparison of DIA workflows on Orbitrap instruments published so far in the field of proteomics. Using a standard human 48 proteins  ...[more]

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