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PXD001428

PXD001428 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMultiple protease based human phosphopeptide atlas
DescriptionSite-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.
HostingRepositoryPRIDE
AnnounceDate2015-05-29
AnnouncementXMLSubmission_2016-01-06_02:13:03.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD001428
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterPiero Giansanti
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListOxidation; Phospho; Acetyl; Carbamidomethyl
InstrumentOrbitrap Fusion; LTQ Orbitrap Elite
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-10-22 02:15:23ID requested
12015-05-29 11:56:18announced
22016-01-06 02:13:04announcedUpdated publication reference for PubMed record(s): 26074081.
Publication List
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, 11(11):1834-43(2015) [pubmed]
Keyword List
curator keyword: Technical, Highlighted
submitter keyword: phosphorylation, kinase, mass spectrometry, proteases
Contact List
Albert J. R. Heck,
contact affiliationBiomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
contact emailA.J.R.Heck@uu.nl
lab head
Piero Giansanti
contact affiliationNPC
contact emailp.giansanti@uu.nl
dataset submitter
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Dataset FTP location
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