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PXD032945 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePhosphoProtein-Peptide Turnover Profiling, validation
DescriptionWe combined pulsed stable isotope labeling of amino acids (pSILAC) with enrichment of phosphorylated peptides in a method we term PhosphoProtein-Peptide Turnover Profiling (PhosphoPPToP). We applied the method to HeLa cells to find peptides whose clearance rates differ from the protein median. Using theoretical modelling, we show that readouts from PPToP are primarily defined by the wiring of the PTM-modification network and not by effects of the PTM on a protein's proteolytic stability. Thus PPToP can be used to identify PTMs occurring, e.g., preferentially early or late in a protein's lifetime. This enables identification of, e.g., protein maturation or protein complex assembly intermediates. This dataset covers experimental testing of identified phosphosites with PPToP. Here, proteins of interest are expressed as GFP-fusion constructs in HeLa cells and subjected to a SILAC pulse. Thereafter, proteins are pulled-down with anti-GFP beads to isolate the exogenously expressed constructs. We multiplex SILAC timepoints from wild-type and mutant constructs for every given protein of interest using TMT16.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListisotope labeled residue; acetylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-04-02 14:02:12ID requested
12022-12-02 06:32:35announced
Publication List
Keyword List
submitter keyword: AP-MS, post-translational modification, protein maturation, GFP-fusion, pull-down, SILAC, protein turnover, phosphorylation,Mass spectrometry, TMT16
Contact List
contact affiliationGenome Biology Unit and Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
contact emailmikhail.savitski@embl.de
lab head
contact affiliationGenome Biology Unit and Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
contact emailhenrik.hammaren@embl.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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