PXD003808

PXD003808 is an original dataset announced via ProteomeXchange.

Title	Phosphoproteomics scaled-down to tumor biopsy level -part 1 cell line
Description	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.
HostingRepository	PRIDE
AnnounceDate	2022-03-02
AnnouncementXML	Submission_2022-03-02_02:53:07.966.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sander Piersma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-03-18 00:48:49	ID requested
⏵ 1	2022-03-02 02:53:08	announced

Dataset with its publication pending

curator keyword: Biological, Biomedical

submitter keyword: Human, CRC, biopsy, colorectal cancer, label-free, single-shot, pTyr, phosphoproteomics

Connie Ramona Jimenez
contact affiliation	OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
contact email	c.jimenez@vumc.nl
lab head
Sander Piersma
contact affiliation	OncoProteomics Laboratory, dept of Medical Oncology, VUmc Medical Center, Amsterdam, The Netherlands
contact email	s.piersma@vumc.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/03/PXD003808

PRIDE project URI

• PRIDE
  1. PXD003808
     1. Label: PRIDE project
     2. Name: Phosphoproteomics scaled-down to tumor biopsy level -part 1 cell line