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PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data

Mass spectrometry-based proteomics methods are widely used to identify and quantify protein complexes involved in diverse biological processes. Specifically, tandem mass spectrometry methods represent an accurate and sensitive strategy for identifying protein-protein interactions. However, most of t...

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Autores principales: González-Avendaño, Mariela, Zúñiga-Almonacid, Simón, Silva, Ian, Lavanderos, Boris, Robinson, Felipe, Rosales-Rojas, Roberto, Durán-Verdugo, Fabio, González, Wendy, Cáceres, Mónica, Cerda, Oscar, Vergara-Jaque, Ariela
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8281810/
https://www.ncbi.nlm.nih.gov/pubmed/34277709
http://dx.doi.org/10.3389/fmolb.2021.701477
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author González-Avendaño, Mariela
Zúñiga-Almonacid, Simón
Silva, Ian
Lavanderos, Boris
Robinson, Felipe
Rosales-Rojas, Roberto
Durán-Verdugo, Fabio
González, Wendy
Cáceres, Mónica
Cerda, Oscar
Vergara-Jaque, Ariela
author_facet González-Avendaño, Mariela
Zúñiga-Almonacid, Simón
Silva, Ian
Lavanderos, Boris
Robinson, Felipe
Rosales-Rojas, Roberto
Durán-Verdugo, Fabio
González, Wendy
Cáceres, Mónica
Cerda, Oscar
Vergara-Jaque, Ariela
author_sort González-Avendaño, Mariela
collection PubMed
description Mass spectrometry-based proteomics methods are widely used to identify and quantify protein complexes involved in diverse biological processes. Specifically, tandem mass spectrometry methods represent an accurate and sensitive strategy for identifying protein-protein interactions. However, most of these approaches provide only lists of peptide fragments associated with a target protein, without performing further analyses to discriminate physical or functional protein-protein interactions. Here, we present the PPI-MASS web server, which provides an interactive analytics platform to identify protein-protein interactions with pharmacological potential by filtering a large protein set according to different biological features. Starting from a list of proteins detected by MS-based methods, PPI-MASS integrates an automatized pipeline to obtain information of each protein from freely accessible databases. The collected data include protein sequence, functional and structural properties, associated pathologies and drugs, as well as location and expression in human tissues. Based on this information, users can manipulate different filters in the web platform to identify candidate proteins to establish physical contacts with a target protein. Thus, our server offers a simple but powerful tool to detect novel protein-protein interactions, avoiding tedious and time-consuming data postprocessing. To test the web server, we employed the interactome of the TRPM4 and TMPRSS11a proteins as a use case. From these data, protein-protein interactions were identified, which have been validated through biochemical and bioinformatic studies. Accordingly, our web platform provides a comprehensive and complementary tool for identifying protein-protein complexes assisting the future design of associated therapies.
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spelling pubmed-82818102021-07-16 PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data González-Avendaño, Mariela Zúñiga-Almonacid, Simón Silva, Ian Lavanderos, Boris Robinson, Felipe Rosales-Rojas, Roberto Durán-Verdugo, Fabio González, Wendy Cáceres, Mónica Cerda, Oscar Vergara-Jaque, Ariela Front Mol Biosci Molecular Biosciences Mass spectrometry-based proteomics methods are widely used to identify and quantify protein complexes involved in diverse biological processes. Specifically, tandem mass spectrometry methods represent an accurate and sensitive strategy for identifying protein-protein interactions. However, most of these approaches provide only lists of peptide fragments associated with a target protein, without performing further analyses to discriminate physical or functional protein-protein interactions. Here, we present the PPI-MASS web server, which provides an interactive analytics platform to identify protein-protein interactions with pharmacological potential by filtering a large protein set according to different biological features. Starting from a list of proteins detected by MS-based methods, PPI-MASS integrates an automatized pipeline to obtain information of each protein from freely accessible databases. The collected data include protein sequence, functional and structural properties, associated pathologies and drugs, as well as location and expression in human tissues. Based on this information, users can manipulate different filters in the web platform to identify candidate proteins to establish physical contacts with a target protein. Thus, our server offers a simple but powerful tool to detect novel protein-protein interactions, avoiding tedious and time-consuming data postprocessing. To test the web server, we employed the interactome of the TRPM4 and TMPRSS11a proteins as a use case. From these data, protein-protein interactions were identified, which have been validated through biochemical and bioinformatic studies. Accordingly, our web platform provides a comprehensive and complementary tool for identifying protein-protein complexes assisting the future design of associated therapies. Frontiers Media S.A. 2021-07-01 /pmc/articles/PMC8281810/ /pubmed/34277709 http://dx.doi.org/10.3389/fmolb.2021.701477 Text en Copyright © 2021 González-Avendaño, Zúñiga-Almonacid, Silva, Lavanderos, Robinson, Rosales-Rojas, Durán-Verdugo, González, Cáceres, Cerda and Vergara-Jaque. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
González-Avendaño, Mariela
Zúñiga-Almonacid, Simón
Silva, Ian
Lavanderos, Boris
Robinson, Felipe
Rosales-Rojas, Roberto
Durán-Verdugo, Fabio
González, Wendy
Cáceres, Mónica
Cerda, Oscar
Vergara-Jaque, Ariela
PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data
title PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data
title_full PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data
title_fullStr PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data
title_full_unstemmed PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data
title_short PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data
title_sort ppi-mass: an interactive web server to identify protein-protein interactions from mass spectrometry-based proteomics data
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8281810/
https://www.ncbi.nlm.nih.gov/pubmed/34277709
http://dx.doi.org/10.3389/fmolb.2021.701477
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