PXD004415

PXD004415 is an original dataset announced via ProteomeXchange.

Title	Quantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells
Description	Reversible protein phosphorylation is one of the most important posttranslational modifications (PTMs) due to its vital role in cellular functions and signaling pathways. Protein phosphorylation is also known to be involved in the regulation of apoptosis. Previously, we have performed a SILAC-based analysis of phosphotyrosinylation of cisplatin-induced apoptotic Jurkat T cells. To further expand this study, we used the same experimental setup and analyzed the global phosphorylation profile. The different steps of the phosphopeptide enrichment protocol using TiO2 beads were tested and the best approach was applied in combination with LC-MS with different normalized collision energy (NCE) values for HCD fragmentation. In total, more than 2,000 phosphoproteins of more than 4,000 phosphopeptides were identified in the four biological replicates of both states. HCD with NCE 25 accounted for 64% and NCE 35 for 36 % of identified phosphopeptides. 425 phosphopeptides were found to be significantly regulated in cisplatin-treated against control samples. KEGG pathway analysis revealed splicosomal proteins and the MAPK signaling pathway to be upregulated and cell cycle proteins to be downregulated. The transcription factors Atf2 and Jun, which are both involved in the MAPK signaling pathway, were further investigated. For Jun, more than 90 spectral counts were found only in apoptotic cells and covered the well-known stress induced phosphorylation sites at S-63/S-73, as well as S-243 which reduces the ability to bind DNA and is required for GSK3 mediated ubiquitinylation at S-239. For Atf2, more than 60 spectral counts were found in apoptotic cells vs. 8 in control cells. Most significantly upregulated sites for Atf2 have been identified at S-90 and S-112, which are less well studied phosphorylation sites of Atf2 as several other sites. Western blot analyses using non-phosphorylated and phosphorylated antibodies were performed to validate the phosphorylation events of Jun and Atf2. Our findings contribute to the current knowledge of the phosphorylation profiles of apoptotic cells.
HostingRepository	PRIDE
AnnounceDate	2017-05-11
AnnouncementXML	Submission_2017-05-11_01:57:33.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD004415
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Trung Tran
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Phospho; Propionamide; Oxidation; Acetyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-22 02:17:51	ID requested
⏵ 1	2017-05-11 01:57:36	announced

Tran TT, Strozynski M, Thiede B, Quantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells. Proteomics, 17(11):(2017) [pubmed]

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

curator keyword: Biological

submitter keyword: : apoptosis, cisplatin, mass spectrometry, phosphoproteomics, phosphorylation

Bernd Thiede
contact affiliation	Proteomics Lab Department of Bioscience Faculty of Mathematic and Natural Science University of Oslo Norway
contact email	bernd.thiede@ibv.uio.no
lab head
Trung Tran
contact affiliation	University of Oslo
contact email	trung.tran@ibv.uio.no
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004415
     1. Label: PRIDE project
     2. Name: Quantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells