PXD014222

PXD014222 is an original dataset announced via ProteomeXchange.

Title	Proteogenomics of colorectal cancer liver metastases
Description	Colorectal cancer (CRC) is the third most common and second most deadly cancer worldwide. Treatments for metastatic CRC (mCRC) are still largely based on toxic chemotherapy regimens, but important insights into tumor biology enabled the development of targeted cancer therapies. Here, we describe a proteogenomic analysis of CRC liver metastases (metastatic CRC, mCRC), an ideal setting to analyze therapeutic resistance which occurs in a short time frame. We selected liver metastases from two CRC patients on both of which we performed deep proteome profiling and WES and RNAseq-directed database searches, identifying 10 predicted muttaions, one of which was KRAS G12V. finding we generated targeted parallel reaction monitoring (PRM) assays using stable isotope labelled standard (SIS) peptides to quantify the actual concentration (fmol per µg of total protein) of the mutated and canonical (wildtype) protein variants for 8 different mutations. We demonstrate on a total of 8 tumor and 6 paired healthy tissue samples (7 and 6 out of these KRASG12V) that PRM allows quantifying the actual mutation rate on the protein level from as little 10 µg of total protein starting amount and within a single 1 hour nano-LC-MS/MS run.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:55:31.369.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bernhard Blank-Landeshammer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-12 00:08:02	ID requested
1	2019-12-04 04:11:16	announced
2	2020-01-15 02:26:35	announced	2020-01-15: Updated publication reference for PubMed record(s): 31805664.
⏵ 3	2024-10-22 04:55:37	announced	2024-10-22: Updated project metadata.

10.3390/cancers11121907;

Blank-Landeshammer B, Richard VR, Mitsa G, Marques M, LeBlanc A, Kollipara L, Feldmann I, Couetoux du Tertre M, Gambaro K, McNamara S, Spatz A, Zahedi RP, Sickmann A, Batist G, Borchers CH, Proteogenomics of Colorectal Cancer Liver Metastases: Complementing Precision Oncology with Phenotypic Data. Cancers (Basel), 11(12):(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Human, LC-MSMS, PRM, Colorectal Cancer, Proteogenomics

Albert Sickmann
contact affiliation	Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
contact email	sickmann@isas.de
lab head
Bernhard Blank-Landeshammer
contact affiliation	Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund
contact email	bernhard.blank@mailbox.org
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/2019/12/PXD014222

PRIDE project URI

• PRIDE
  1. PXD014222
     1. Label: PRIDE project
     2. Name: Proteogenomics of colorectal cancer liver metastases