MassIVE MSV000096198

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SysQuan: repurposing SILAC mice for affordable absolute quantitation of the human proteome

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Description

We have repurposed SILAC mouse tissues/biofluids as system-wide internal standards for matched human samples to enable absolute quantitation (AbsQuan) of theoretically >2/3 of the human proteome using 132,380 shared tryptic peptides. We demonstrate that SysQuan enables quantifying 70% and 31% of the largest liver and plasma reference proteomes, respectively. We exemplify for 14 metabolic proteins that abundant standard isotope labeled mouse tissues enable cost-effective reverse AbsQuan in - theoretically 1000s of - human samples. Moreover, 10,000s of light/heavy doublets in untargeted SysQuan datasets enable unique post-acquisition AbsQuan. [doi:10.25345/C5QF8JX08] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: absolute quantitation ; cross species ; silac ; DatasetType:Proteomics

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Principal Investigators:
(in alphabetical order) 		Rene Zahedi, University of Manitoba, Canada
Submitting User: vspicer1
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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.

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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.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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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.