PXD000414

PXD000414 is an original dataset announced via ProteomeXchange.

Title	Quantitiative phosphoproteomic analysis of SKS1 signaling network involved in yeast filamentous growth by LC-MS in combination with SILAC
Description	Yeast pseudohyphal growth(filamentous growth) is regulated by signaling pathways responsive to nitrogen stress and glucose deprivation, but the molecular link between pseudohyphal filamentation and glucose signaling is not fully understood. To identify the Sks1p signaling network involved in filamentous growth, we applied mass spectrometry-based quantitative phosphoproteomics in combination with SILAC. We investigated differential protein expressions and changes in phosphorylation levels in SKS1 kinase dead mutant yeast cells (SKS1-KD, Lys-4 and Arg-6 labeled) under filamentous growth condition. Twelve SCX fractions of SILAC paired peptides derived from SKS1-KD and wild type yeast cells were subjected to phosphopeptide enrichment by using ZrO2, prior to LC-MSMS by an LTQ-Orbitrap. MaxQunat (ver 1.0.13.8) package incorporating Mascot search was used for identification and quantification of peptides and proteins. RAW files were searched against a composite target-decoy database containing yeast ORFs from SGD allowing variable modifications of phospho (STY) and oxi (M) and a fixed modification of carbamidomethyl(C) within 7 ppm (MS) and 0.5 Da (MSMS) mass tolerances. Peptide and protein identifications were maintained within 5% FDR.
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_01:32:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hye Kyong Kweon
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	6x(13)C: 4x(15)N labeled L-arginine; monohydroxylated residue; iodoacetamide derivatized residue; phosphorylated residue; 6x(13)C labeled L-arginine; 6x(13)C: 2x(15)N labeled L-lysine; (4: 4
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-08-14 07:27:15	ID requested
1	2014-04-16 13:22:34	announced
⏵ 2	2014-07-25 01:32:33	announced	Updated project metadata.

Johnson C, Kweon HK, Sheidy D, Shively CA, Mellacheruvu D, Nesvizhskii AI, Andrews PC, Kumar A, The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response. PLoS Genet, 10(3):e1004183(2014) [pubmed]

submitter keyword: Saccharomyces cerevisiae, SKS1, filamentous growth, LC-MS, phosphoproteome, SILAC,

Hye Kyong Kweon
contact affiliation	Department of Biological Chemistry
contact email	hkweon@umich.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000414
     1. Label: PRIDE project
     2. Name: Quantitiative phosphoproteomic analysis of SKS1 signaling network involved in yeast filamentous growth by LC-MS in combination with SILAC