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Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry

Since the start of mass-spectrometry-based proteomics, proteins from non-referenced open reading frames or alternative proteins (AltProts) have been overlooked. Here, we present a protocol to identify human subcellular AltProt and decipher some interactions using cross-linking mass spectrometry. We...

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Detalles Bibliográficos
Autores principales: Garcia-del Rio, Diego Fernando, Fournier, Isabelle, Cardon, Tristan, Salzet, Michel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10511867/
https://www.ncbi.nlm.nih.gov/pubmed/37384523
http://dx.doi.org/10.1016/j.xpro.2023.102380
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author Garcia-del Rio, Diego Fernando
Fournier, Isabelle
Cardon, Tristan
Salzet, Michel
author_facet Garcia-del Rio, Diego Fernando
Fournier, Isabelle
Cardon, Tristan
Salzet, Michel
author_sort Garcia-del Rio, Diego Fernando
collection PubMed
description Since the start of mass-spectrometry-based proteomics, proteins from non-referenced open reading frames or alternative proteins (AltProts) have been overlooked. Here, we present a protocol to identify human subcellular AltProt and decipher some interactions using cross-linking mass spectrometry. We describe steps for cell culture, in cellulo cross-link, subcellular extraction, and sequential digestion. We then detail both liquid chromatography-tandem mass spectrometry and cross-link data analyses. The implementation of a single workflow allows the non-targeted identification of signaling pathways involving AltProts. For complete details on the use and execution of this protocol, please refer to Garcia-del Rio et al.(1)
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spelling pubmed-105118672023-09-22 Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry Garcia-del Rio, Diego Fernando Fournier, Isabelle Cardon, Tristan Salzet, Michel STAR Protoc Protocol Since the start of mass-spectrometry-based proteomics, proteins from non-referenced open reading frames or alternative proteins (AltProts) have been overlooked. Here, we present a protocol to identify human subcellular AltProt and decipher some interactions using cross-linking mass spectrometry. We describe steps for cell culture, in cellulo cross-link, subcellular extraction, and sequential digestion. We then detail both liquid chromatography-tandem mass spectrometry and cross-link data analyses. The implementation of a single workflow allows the non-targeted identification of signaling pathways involving AltProts. For complete details on the use and execution of this protocol, please refer to Garcia-del Rio et al.(1) Elsevier 2023-06-28 /pmc/articles/PMC10511867/ /pubmed/37384523 http://dx.doi.org/10.1016/j.xpro.2023.102380 Text en © 2023 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Garcia-del Rio, Diego Fernando
Fournier, Isabelle
Cardon, Tristan
Salzet, Michel
Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry
title Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry
title_full Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry
title_fullStr Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry
title_full_unstemmed Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry
title_short Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry
title_sort protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10511867/
https://www.ncbi.nlm.nih.gov/pubmed/37384523
http://dx.doi.org/10.1016/j.xpro.2023.102380
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