Functional Analysis of MS-Based Proteomics Data: From Protein Groups to Networks

Marie Locard-Paulet; Nadezhda T. Doncheva; John H. Morris; Lars Juhl Jensen

doi:10.1016/j.mcpro.2024.100871

Functional Analysis of MS-Based Proteomics Data: From Protein Groups to Networks

Marie Locard-Paulet^*, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen^*

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Abstract

Mass spectrometry-based proteomics allows the quantification of thousands of proteins, protein variants, and their modifications, in many biological samples. These are derived from the measurement of peptide relative quantities, and it is not always possible to distinguish proteins with similar sequences due to the absence of protein-specific peptides. In such cases, peptide signals are reported in protein groups that can correspond to several genes. Here, we show that multi-gene protein groups have a limited impact on GO-term enrichment, but selecting only one gene per group affects network analysis. We thus present the Cytoscape app Proteo Visualizer (https://apps.cytoscape.org/apps/ProteoVisualizer) that is designed for retrieving protein interaction networks from STRING using protein groups as input and thus allows visualization and network analysis of bottom-up MS-based proteomics data sets.

Originalsprog	Engelsk
Artikelnummer	100871
Tidsskrift	Molecular and Cellular Proteomics
Vol/bind	23
Udgave nummer	12
Antal sider	14
ISSN	1535-9476
DOI	https://doi.org/10.1016/j.mcpro.2024.100871
Status	Udgivet - 2024

Bibliografisk note

Funding Information:
N. T. D and L. J. J were funded by the Novo Nordisk Foundation (NNF14CC0001). M. L.-P. was funded by the French Ministry of Research with the Investissement d\u2019Avenir Infrastructures Nationales en Biologie et Sant\u00E9 program (ProFI, Proteomics French Infrastructure project, ANR-10-INBS-08). J. H. M is funded by NIGMS grant P41 GM103504 and NHGRI grant U24 HG012107.

Publisher Copyright:
© 2024 THE AUTHORS.

Adgang til dokumentet

10.1016/j.mcpro.2024.100871Licens: CC BY

FulltextForlagets udgivne version, 2,14 MBLicens: CC BY

Citationsformater

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AB - Mass spectrometry-based proteomics allows the quantification of thousands of proteins, protein variants, and their modifications, in many biological samples. These are derived from the measurement of peptide relative quantities, and it is not always possible to distinguish proteins with similar sequences due to the absence of protein-specific peptides. In such cases, peptide signals are reported in protein groups that can correspond to several genes. Here, we show that multi-gene protein groups have a limited impact on GO-term enrichment, but selecting only one gene per group affects network analysis. We thus present the Cytoscape app Proteo Visualizer (https://apps.cytoscape.org/apps/ProteoVisualizer) that is designed for retrieving protein interaction networks from STRING using protein groups as input and thus allows visualization and network analysis of bottom-up MS-based proteomics data sets.

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