MSCI: an open-source Python package for information content assessment of peptide fragmentation spectra
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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 2025-10-06T06:27:44Z
- dc.date.available 2025-10-06T06:27:44Z
- dc.date.issued 2025
- dc.description.abstract Motivation: In mass spectrometry-based proteomics, the availability of peptide prior knowledge has improved our ability to assign fragmentation spectra to specific peptide sequences. However, some peptides exhibit similar analytical values and fragmentation patterns, which makes them nearly indistinguishable with current data analysis tools. Results: Here we developed the Mass Spectrometry Content Information (MSCI) Python package to tackle the challenges of peptide identification in mass spectrometry-based proteomics, particularly regarding indistinguishable peptides. MSCI provides a comprehensive toolset that streamlines the workflow from data import to spectral analysis, enabling researchers to effectively evaluate fragmentation similarity scores among peptide sequences and pinpoint indistinguishable peptide pairs in a given proteome. Availability and implementation: MSCI is implemented in Python and it is released under a permissive MIT license. The source code and the installers are available on GitHub at https://github.com/proteomicsunitcrg/MSCI.
- dc.description.sponsorship This work was supported by the Spanish Ministry of Science, Innovation and Universities [PID2020-115092GB-I00, AEI/10.13039/501100011033], the Departament de Recerca i Universitats de la Generalitat de Catalunya [2021SGR01225]; and the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Actions—European Training Networks PROTrEIN: Computational Proteomics Training European Innovative Network [956148]. The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS OmicsTech). We also acknowledge support of the Spanish Ministry of Science and Innovation through the Centro de Excelencia Severo Ochoa (CEX2020-001049-S, MCIN/AEI /10.13039/501100011033), and the Generalitat de Catalunya through the CERCA programme.
- dc.format.mimetype application/pdf
- dc.identifier.citation Elhamraoui Z, Borràs E, Wilhelm M, Sabidó E. MSCI: an open-source Python package for information content assessment of peptide fragmentation spectra. Bioinform Adv. 2025 May 24;5(1):vbaf125. DOI: 10.1093/bioadv/vbaf125
- dc.identifier.doi http://dx.doi.org/10.1093/bioadv/vbaf125
- dc.identifier.issn 2635-0041
- dc.identifier.uri http://hdl.handle.net/10230/71391
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Bioinform Adv. 2025 May 24;5(1):vbaf125
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/956148
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-115092GB-I00
- dc.rights © The Author(s) 2025. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.other Pèptids
- dc.title MSCI: an open-source Python package for information content assessment of peptide fragmentation spectra
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion