Proteogenomics and Differential Ion Mobility Enable the Exploration of the Mutational Landscape in Colon Cancer Cells.

Autor:	Wu Z; Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec 514 343-6910, Canada.; Department of Chemistry, Université de Montréal, Montréal, Quebec 514 343-6910, Canada., Bonneil É; Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec 514 343-6910, Canada., Belford M; ThermoFisher Scientific, San Jose, California 95134, United States., Boeser C; ThermoFisher Scientific, San Jose, California 95134, United States., Ruiz Cuevas MV; Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec 514 343-6910, Canada.; Department of Biochemistry, Université de Montréal, Montréal, Quebec 514 343-6910, Canada., Lemieux S; Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec 514 343-6910, Canada.; Department of Biochemistry, Université de Montréal, Montréal, Quebec 514 343-6910, Canada., Dunyach JJ; ThermoFisher Scientific, San Jose, California 95134, United States., Thibault P; Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec 514 343-6910, Canada.; Department of Chemistry, Université de Montréal, Montréal, Quebec 514 343-6910, Canada.
Jazyk:	angličtina
Zdroj:	Analytical chemistry [Anal Chem] 2022 Sep 06; Vol. 94 (35), pp. 12086-12094. Date of Electronic Publication: 2022 Aug 22.
DOI:	10.1021/acs.analchem.2c02056
Abstrakt:	The sensitivity and depth of proteomic analyses are 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 and 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 more than 60% 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 data sets.
Databáze:	MEDLINE
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