New ProteomeXchange dataset PXD044389

[ProteomeCentral Agent]

Dear ProteomeXchange subscriber, a new ProteomeXchange dataset is being announced. To see more information, click here:

https://proteomecentral.proteomexchange.org/dataset/PXD044389

Summary of dataset

Status: new
Identifier: PXD044389
HostingRepository: PRIDE
Species: Homo sapiens
Title: Expansive Genomic Mapping of Mutant Peptides and Characterisation of Allelic Bias in Cancer Cell Lines
Submitter: Yasset Perez-Riverol
LabHead: Jyoti S
Description: Investigation of non-synonymous mutation as a major driver for cancer is essential for discovery of biomarkers and therapeutics. Although, many cancer-associated mutations have been identified through genomics, there is a poor understanding of how they manifest in the proteome. In fact, detection of mutation derived peptides is confounded by technical and biological factors. In this study cancer associated mutations from the COSMIC database were integrated into proteins, to generate cell line specific sequence databases. We used a robust workflow for high-throughput processing of 375 cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) to identify mutant peptides and generate PRIDE compatible mzTab results. This includes a peptide to genome mapping tool, PepGenome, allowing targeted mapping of mutant peptides. Examining the allelic paired non-mutant reference peptides, we were able to profile significantly more potential mutant peptides and determine allelic b
iases in the expression and observation of mutant peptides. We present quantification, genomic mapping, and evaluation of 1,336 cancer associated mutant peptides and infer protein allelic bias for 31,219 mutations in. We highlight the problems faced in detecting and characterising mutant peptides by mass spectrometry and show that allelic bias plays a significant role in suppressing the expression of mutant proteoforms.

HTML_URL: https://proteomecentral.proteomexchange.org/dataset/PXD044389
XML_URL: https://proteomecentral.proteomexchange.org/dataset/PXD044389&outputMode=XML