Utilising precursor ion connectivity of different charge states to improve peptide and protein identification in MS/MS analysis

Adair, L. R., Jones, I. ORCID: https://orcid.org/0000-0002-7738-2516 and Cramer, R. ORCID: https://orcid.org/0000-0002-8037-2511 (2024) Utilising precursor ion connectivity of different charge states to improve peptide and protein identification in MS/MS analysis. Analytical Chemistry, 96 (3). pp. 985-990. ISSN 0003-2700 doi: 10.1021/acs.analchem.3c03061

Abstract/Summary

Tandem mass spectrometry (MS/MS) has become a key method for the structural analysis of biomolecules such as peptide and proteins. A pervasive problem in MS/MS analyses, especially for top-down proteomics, is the occurrence of chimeric spectra, when two or more precursor ions are co-isolated and fragmented, thus leading to complex MS/MS spectra that are populated with fragment ions originating from different precursor ions. This type of convoluted data typically results in low sequence database search scores due to the vast number of mixed-source fragment ions, of which only a fraction originates from a specific precursor ion. Herein, we present a novel workflow that deconvolutes the data of chimeric MS/MS spectra, improving the protein search scores and sequence coverages in database searching and thus providing a more confident peptide and protein identification. Previously misidentified proteins or proteins with insignificant search scores can be correctly and significantly identified following the presented data acquisition and analysis workflow with search scores increasing by a factor of 3-4 for smaller precursor ions (peptides) and >6 for larger precursor ions such as intact ubiquitin and cytochrome C.

Item Type	Article
URI	https://reading-clone.eprints-hosting.org/id/eprint/114640
Identification Number/DOI	10.1021/acs.analchem.3c03061
Refereed	Yes
Divisions	Life Sciences > School of Chemistry, Food and Pharmacy > Department of Chemistry
Publisher	American Chemical Society
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