PXD044389

PXD044389 is an original dataset announced via ProteomeXchange.

Title	Expansive Genomic Mapping of Mutant Peptides and Characterisation of Allelic Bias in Cancer Cell Lines
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 biases 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.
HostingRepository	PRIDE
AnnounceDate	2025-12-18
AnnouncementXML	Submission_2025-12-18_07:35:34.580.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD044389
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yasset Perez-Riverol
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-05 08:53:54	ID requested
⏵ 1	2025-12-18 07:35:35	announced

10.6019/PXD044389;

submitter keyword: None

Jyoti S
contact affiliation	The Institute of Cancer Research, London, SW3 6JB, UK
contact email	jyoti.choudhary@icr.ac.uk
lab head
Yasset Perez-Riverol
contact affiliation	EBI
contact email	yperez@ebi.ac.uk
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/2025/12/PXD044389

PRIDE project URI

• PRIDE
  1. PXD044389
     1. Label: PRIDE project
     2. Name: Expansive Genomic Mapping of Mutant Peptides and Characterisation of Allelic Bias in Cancer Cell Lines