Proteogenomics and differential ion mobility enables the exploration of the mutational landscape in colon cancer cells

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Eric Bonneil  

LAB HEAD: Pierre Thibault

PROVIDER: PXD033710 | Pride | 2023-02-21

REPOSITORIES: Pride