PXD033710

PXD033710 is an original dataset announced via ProteomeXchange.

Title	Proteogenomics and differential ion mobility enables the exploration of the mutational landscape in colon cancer cells
Description	The sensitivity and depth of proteomic analyses is limited by isobaric ions and interferences that preclude the identification of low abundance peptides. Extensive sample fractionation is often required to extend proteome coverage when sample amount is not a limitation. Ion mobility devices provide a viable alternate approach to resolve confounding ions, improve peak capacity and mass spectrometry (MS) sensitivity. Here, we report the integration of differential ion mobility with segmented ion fractionation (SIFT) to enhance the comprehensiveness of proteomic analyses. The combination of differential ion mobility and SIFT, where narrow windows of ~ m/z 100 are acquired in turn, is found particularly advantageous in the analysis of protein digests, and typically provided 70% gain in identification compared to conventional single-shot LC-MS/MS. The application of this approach is further demonstrated for the analysis of tryptic digests from different colorectal cancer cell lines where the enhanced sensitivity enabled the identification of single amino acid variants that were correlated with the corresponding transcriptomic datasets.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:31:35.220.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD033710
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Eric Bonneil
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-05 01:18:45	ID requested
1	2023-02-21 09:47:10	announced
⏵ 2	2023-11-14 07:31:36	announced	2023-11-14: Updated project metadata.

10.6019/PXD033710;

Wu Z, Bonneil É, Belford M, Boeser C, Ruiz Cuevas MV, Lemieux S, Dunyach JJ, Thibault P, Proteogenomics and Differential Ion Mobility Enable the Exploration of the Mutational Landscape in Colon Cancer Cells. Anal Chem, 94(35):12086-12094(2022) [pubmed]

submitter keyword: gas-phase fractionation, single amino acid polymorphism, proteogenomics, protein mutation, mass spectrometry, colon cancer, single amino acid variant,High field asymmetric waveform ion mobility (FAIMS)

Pierre Thibault
contact affiliation	IRIC-Université de Montréal
contact email	pierre.thibault@umontreal.ca
lab head
Eric Bonneil
contact affiliation	Proteomic Platform
contact email	eric.bonneil@umontreal.ca
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/2023/02/PXD033710

PRIDE project URI

• PRIDE
  1. PXD033710
     1. Label: PRIDE project
     2. Name: Proteogenomics and differential ion mobility enables the exploration of the mutational landscape in colon cancer cells