Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics

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...

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Detalles Bibliográficos
Autores: Elhamraoui, Zahra, Borràs, Eva, Wilhelm, Mathias, Sabidó Aguadé, Eduard, 1981-
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/68925
Acceso en línea:http://hdl.handle.net/10230/68925
http://dx.doi.org/10.1021/acs.analchem.4c02803
Access Level:acceso abierto
Palabra clave:Fragmentation
Monomers
Peptide identification
Peptides and proteins
Precursors
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spelling Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomicsElhamraoui, ZahraBorràs, EvaWilhelm, MathiasSabidó Aguadé, Eduard, 1981-FragmentationMonomersPeptide identificationPeptides and proteinsPrecursorsMass-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.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).American Chemical Society (ACS)202420242024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/68925http://dx.doi.org/10.1021/acs.analchem.4c02803reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésAnal Chem. 2024 Oct 8;96(40):15829-33info:eu-repo/grantAgreement/EC/H2020/956148info:eu-repo/grantAgreement/ES/2PE/PID2020-115092GB-I00This publication is licensed under CC-BY 4.0 (http://creativecommons.org/licenses/by/4.0/).http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/689252026-05-29T05:05:01Z
dc.title.none.fl_str_mv Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
title Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
spellingShingle Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
Elhamraoui, Zahra
Fragmentation
Monomers
Peptide identification
Peptides and proteins
Precursors
title_short Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
title_full Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
title_fullStr Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
title_full_unstemmed Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
title_sort Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
dc.creator.none.fl_str_mv Elhamraoui, Zahra
Borràs, Eva
Wilhelm, Mathias
Sabidó Aguadé, Eduard, 1981-
author Elhamraoui, Zahra
author_facet Elhamraoui, Zahra
Borràs, Eva
Wilhelm, Mathias
Sabidó Aguadé, Eduard, 1981-
author_role author
author2 Borràs, Eva
Wilhelm, Mathias
Sabidó Aguadé, Eduard, 1981-
author2_role author
author
author
dc.subject.none.fl_str_mv Fragmentation
Monomers
Peptide identification
Peptides and proteins
Precursors
topic Fragmentation
Monomers
Peptide identification
Peptides and proteins
Precursors
description 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.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/68925
http://dx.doi.org/10.1021/acs.analchem.4c02803
url http://hdl.handle.net/10230/68925
http://dx.doi.org/10.1021/acs.analchem.4c02803
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Anal Chem. 2024 Oct 8;96(40):15829-33
info:eu-repo/grantAgreement/EC/H2020/956148
info:eu-repo/grantAgreement/ES/2PE/PID2020-115092GB-I00
dc.rights.none.fl_str_mv This publication is licensed under CC-BY 4.0 (http://creativecommons.org/licenses/by/4.0/).
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv This publication is licensed under CC-BY 4.0 (http://creativecommons.org/licenses/by/4.0/).
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Chemical Society (ACS)
publisher.none.fl_str_mv American Chemical Society (ACS)
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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