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PXD001550

PXD001550 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHuman CRC cell line baseline phosphoproteomics
DescriptionThere is a need for robust phosphopeptide enrichment methods to allow signaling network analysis in cancer cell lines and tissues with minimal fractionation. With recent instrument developments thousands of unique phosphopeptides can be detected by single-shot LC-MS/MS. However, successful phosphoproteomics experiments still rely on efficient phosphopeptide enrichment from a tryptic digest prior to LC-MS/MS analysis. Here we describe a performance assessment of HAMMOC (hydroxyl acid modified metal affinity chromatography) (Sugiyama MCP2007, Kyono, JPR 2008) combined with single shot label-free quantitation at 500 µg peptide input level. We apply the method to profile the baseline phosphorylation landscape of a panel of 8 colorectal cancer (CRC) cell lines. These CRC cell lines represent the 3 CRC subtypes (CCS1, CCS2 and CCS3) as reported by large-scale transcriptome analysis. We report an analysis of the phosphoprotein network and processes enriched in the cell lines representing the poor prognosis CCS3 subtype.
HostingRepositoryPRIDE
AnnounceDate2015-04-15
AnnouncementXMLSubmission_2015-04-15_03:07:32.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSander Piersma
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; phosphorylated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-11-28 00:37:47ID requested
12015-04-15 03:07:33announced
Publication List
Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR, Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines. J Proteomics, 127(Pt B):247-58(2015) [pubmed]
Keyword List
curator keyword: Biomedical, Technical
submitter keyword: Human, CRC, colorectal cancer, label-free, single-shot, phosphoproteomics
Contact List
Connie Ramona Jimenez
contact affiliationOncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
contact emailc.jimenez@vumc.nl
lab head
Sander Piersma
contact affiliationOncoProteomics Laboratory, dept of Medical Oncology, VUmc Medical Center, Amsterdam, The Netherlands
contact emails.piersma@vumc.nl
dataset submitter
Full Dataset Link List
Dataset FTP location
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