MassIVE MSV000080223

Imported Reanalysis Dataset Public PXD001428

Multiple protease based human phosphopeptide atlas

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Description

Site-specific phospho-antibodies are commonly used to study these changes, however only a limited number of good antibodies is available, covering just a few signaling nodes in important pathways. It is highly unlikely that specific antibodies, covering the more than hundred thousands of estimated phosphosites in human cells, will become available soon. Mass spectrometry (MS)-based approaches are becoming of interest, as these are able to monitor at least thousands of sites simultaneously. However, it has become apparent that important signaling nodes, detectable by phosphosite specific-antibodies are quite often not observed in these large-scale in-depth MS-based studies. Here we addressed this issue by using multiple proteases for protein digestion, thereby increasing the size of the accessible and detectable phosphoproteome. We demonstrate that nearly each phosphosite has a preferred protease which favors detection by MS. For specific sites the use of alternative proteases increases the intensity by more than 1,000 fold. Based on the results we define and make publicly available a human phosphopeptide atlas of more than 37,771 unique phosphopeptides, correlating to over 18,000 unique phosphosites, that will be useful for both shot-gun as well as targeted MRM/PRM/SWATH based phosphoproteomics studies. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: phosphorylation ; kinase ; mass spectrometry ; proteases

Contact

Principal Investigators:
(in alphabetical order) 		Dr Albert J. R. Heck,
Submitting User: ccms

Publications

Giansanti P, Aye TT, van den Toorn H, Peng M, van Breukelen B, Heck AJ.
An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas.
Cell Rep. 2015 Jun 23;11(11):1834-43. Epub 2015 Jun 11.

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Identification Results
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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.

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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.