Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal

Schulze, Stefan; Igiraneza, Aime Bienfait; Kösters, Manuel; Leufken, Johannes; Leidel, Sebastian A.; Garcia, Benjamin A.; Fufezan, Christian; Pohlschroder, Mechthild (2021). Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal. Journal of proteome research, 20(4), pp. 1986-1996. American Chemical Society 10.1021/acs.jproteome.0c00799

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The identification of peptide sequences and their post-translational modifications (PTMs) is a crucial step in the analysis of bottom-up proteomics data. The recent development of open modification search (OMS) engines allows virtually all PTMs to be searched for. This not only increases the number of spectra that can be matched to peptides but also greatly advances the understanding of the biological roles of PTMs through the identification, and the thereby facilitated quantification, of peptidoforms (peptide sequences and their potential PTMs). Whereas the benefits of combining results from multiple protein database search engines have been previously established, similar approaches for OMS results have been missing so far. Here we compare and combine results from three different OMS engines, demonstrating an increase in peptide spectrum matches of 8–18%. The unification of search results furthermore allows for the combined downstream processing of search results, including the mapping to potential PTMs. Finally, we test for the ability of OMS engines to identify glycosylated peptides. The implementation of these engines in the Python framework Ursgal facilitates the straightforward application of the OMS with unified parameters and results files, thereby enabling yet unmatched high-throughput, large-scale data analysis.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Kösters, Manuel, Leufken, Johannes, Leidel, Sebastian Andreas

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry

ISSN:

1535-3893

Publisher:

American Chemical Society

Language:

English

Submitter:

Christina Schüpbach

Date Deposited:

07 Apr 2021 17:58

Last Modified:

05 Dec 2022 15:49

Publisher DOI:

10.1021/acs.jproteome.0c00799

PubMed ID:

33514075

BORIS DOI:

10.48350/154175

URI:

https://boris.unibe.ch/id/eprint/154175

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