PXD032945

PXD032945 is an original dataset announced via ProteomeXchange.

Title	PhosphoProtein-Peptide Turnover Profiling, validation
Description	We 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.
HostingRepository	PRIDE
AnnounceDate	2022-12-02
AnnouncementXML	Submission_2022-12-02_06:32:35.505.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	HenrikHammarén
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	isotope labeled residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-02 14:02:12	ID requested
⏵ 1	2022-12-02 06:32:35	announced

submitter keyword: AP-MS, post-translational modification, protein maturation, GFP-fusion, pull-down, SILAC, protein turnover, phosphorylation,Mass spectrometry, TMT16

MikhailSavitski
contact affiliation	Genome Biology Unit and Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
contact email	mikhail.savitski@embl.de
lab head
HenrikHammarén
contact affiliation	Genome Biology Unit and Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
contact email	henrik.hammaren@embl.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD032945
     1. Label: PRIDE project
     2. Name: PhosphoProtein-Peptide Turnover Profiling, validation