MassIVE MSV000087597

Partial Public PXD026600

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

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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). [doi:10.25345/C57C0G] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: DIA workflow ; benchmark ; quantitication ; proteomic standard

Contact

Principal Investigators:
(in alphabetical order) 		Arnaud Droit, CHU de Quebec Universite Laval, Canada
Submitting User: Arno

Publications

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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Experimental Design
    Conditions:
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Identification Results
    Proteins (Human, Remapped):
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Quantification Results
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Species

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When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.