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

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...

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Bibliographic Details
Published in:Analytical chemistry (Washington) 2022-09, Vol.94 (35), p.12086-12094
Main Authors: Wu, Zhaoguan, Bonneil, Éric, Belford, Michael, Boeser, Cornelia, Ruiz Cuevas, Maria Virginia, Lemieux, Sébastien, Dunyach, Jean-Jacques, Thibault, Pierre
Format: Article
Language:English
Subjects:
Amino acids
Chemistry
Chromatography, Liquid - methods
Colon
Colon cancer
Colonic Neoplasms - genetics
Colorectal cancer
Colorectal carcinoma
Fractionation
Humans
Ionic mobility
Ions
Mass spectrometry
Mass spectroscopy
Mobility
Peptides
Proteogenomics
Proteome
Proteomes
Proteomics
Proteomics - methods
Sensitivity enhancement
Tandem Mass Spectrometry - methods
Transcriptomics
Tumor cell lines
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Summary: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.
ISSN:0003-2700
1520-6882
1520-6882
DOI:10.1021/acs.analchem.2c02056