Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
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- dc.contributor.author Elhamraoui, Zahra
- dc.contributor.author Borràs, Eva
- dc.contributor.author Wilhelm, Mathias
- dc.contributor.author Sabidó Aguadé, Eduard, 1981-
- dc.date.accessioned 2024-12-05T07:34:36Z
- dc.date.available 2024-12-05T07:34:36Z
- dc.date.issued 2024
- dc.description.abstract Mass-spectrometry-based proteomics has advanced with the integration of experimental and predicted spectral libraries, which have significantly improved peptide identification in complex search spaces. However, challenges persist in distinguishing some peptides with close retention times and nearly identical fragmentation patterns. In this study, we conducted a theoretical assessment to quantify the prevalence of indistinguishable peptides within the human canonical proteome and immunopeptidome using state-of-the-art retention time and spectrum prediction models. By quantifying the proportion of peptides posing challenges to unequivocal identification, we set the theoretical nonaccessible portion within a given proteome, and underscore the effectiveness of contemporary analytical methodologies in resolving the complexity of the human proteome and immunopeptidome via mass spectrometry.
- dc.description.sponsorship We acknowledge support of the Spanish Ministry of Science and Innovation through the Centro de Excelencia Severo Ochoa (No. CEX2020-001049-S grant funded by MCIN/AEI/10.13039/501100011033) and No. PID2020-115092GB-I00 funded by AEI/10.13039/501100011033, and the Generalitat de Catalunya through the CERCA programme and the Departament de Recerca i Universitats (No. 2021-SGR2021-01225). This result is part of a project that has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 956148. The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS OmicsTech).
- dc.format.mimetype application/pdf
- dc.identifier.citation Elhamraoui Z, Borràs E, Wilhelm M, Sabidó E. Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics. Anal Chem. 2024 Oct 8;96(40):15829-33. DOI: 10.1021/acs.analchem.4c02803
- dc.identifier.doi http://dx.doi.org/10.1021/acs.analchem.4c02803
- dc.identifier.issn 0003-2700
- dc.identifier.uri http://hdl.handle.net/10230/68925
- dc.language.iso eng
- dc.publisher American Chemical Society (ACS)
- dc.relation.ispartof Anal Chem. 2024 Oct 8;96(40):15829-33
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/956148
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-115092GB-I00
- dc.rights This publication is licensed under CC-BY 4.0 (http://creativecommons.org/licenses/by/4.0/).
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.keyword Fragmentation
- dc.subject.keyword Monomers
- dc.subject.keyword Peptide identification
- dc.subject.keyword Peptides and proteins
- dc.subject.keyword Precursors
- dc.title Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion