Description
Mass spectrometry-based proteomics now routinely enables identification of over 10,000 human proteins from a single sample. However, proteins are typically identified by peptide sequences representing about 20% of all proteinogenic amino acids encoded in the transcriptome. Deeper protein sequencing - detection of all amino acids - is imperative for proteoform discovery and quantitative comparison. Here, we utilized six ENCODE cell lines, six proteases, and three tandem mass spectrometry (MS/MS) fragmentation methods to collect 2,491 raw MS data files. From these data we identified 17,717 protein groups with a median sequence coverage of 79.2%, confirming over eight million unique human amino acid residues. We compare our proteomics data with transcriptomics data and demonstrate how such deep proteome coverage can enable detection of over 7,000 proteoforms including 70.9 to 90.6% of all non-synonymous mutations and over 5,000 alternative splicing event junctions. Our dataset represents a valuable resource as the largest human proteome with the highest sequence coverage ever reported.
[doi:10.25345/C5WF83]
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: single amino acid polymorphism ; splice variant ; deep sequencing ; transcriptomics ; proteomics ; fractionation
Contact
Principal Investigators:
(in alphabetical order)
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Joshua Coon, University of Wisconsin - Madison, United States
Juergen Cox, Max Planck Institute of Biochemistry, Germany
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Submitting User: |
coonlabs
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Conditions:
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Biological Replicates:
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Technical Replicates:
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Identification Results |
Proteins (Human, Remapped):
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Proteins (Reported):
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Peptides:
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Variant Peptides:
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PSMs:
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Differential Proteins:
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Quantified Proteins:
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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.
"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.