Dataset Information

Phosphoproteomics scaled-down to tumor biopsy level. Part 2: biopsies

ABSTRACT: Mass spectrometry-based phosphoproteomics of tumor tissue or cell line lysates provides insight in aberrantly activated signaling pathways and potential drug targets. For improved understanding of the individual patient’s tumor biology, analysis of the phosphoproteome should be feasible and reproducible using tumor needle biopsies. We hereto scaled down a pTyr-phosphopeptide enrichment protocol to biopsy-level protein input and show its performance using colorectal cancer (CRC) cell line and needle biopsies from patients. In this study, the feasibility of label-free pTyr-phosphoproteomics at the biopsy level is demonstrated. Unsupervised cluster analysis shows that this approach can identify patient-specific profiles, which will improve our understanding of individual tumor biology and may enable future pTyr-phosphoproteomics-based TKI treatment selection.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Sander Piersma

LAB HEAD: Connie Ramona Jimenez

PROVIDER: PXD003814 | Pride | 2019-10-28

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	LysateSupplementarytablepeptides.xlsx	Xlsx
	LysateSupplementarytableproteins.xlsx	Xlsx
	MxQ_biopsy_pTyr.zip	Other
	QE1_140903_OPL1013_RH_MLA_LYS_biopsy_rep_12.raw	Raw
	QE1_140903_OPL1013_RH_MLA_LYS_biopsy_rep_13.raw	Raw

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Publications

Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection.

Labots Mariette M van der Mijn Johannes C JC Beekhof Robin R Piersma Sander R SR de Goeij-de Haas Richard R RR Pham Thang V TV Knol Jaco C JC Dekker Henk H van Grieken Nicole C T NCT Verheul Henk M W HMW Jiménez Connie R CR

Journal of proteomics 20170423

Mass spectrometry-based phosphoproteomics of cancer cell and tissue lysates provides insight in aberrantly activated signaling pathways and potential drug targets. For improved understanding of individual patient's tumor biology and to allow selection of tyrosine kinase inhibitors in individual patients, phosphoproteomics of small clinical samples should be feasible and reproducible. We aimed to scale down a pTyr-phosphopeptide enrichment protocol to biopsy-level protein input and assess reprodu ...[more]

PMID: 28442448

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