Cargando…
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...
Autores principales: | , , , , , , , , , , |
---|---|
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 |
_version_ | 1783722889965469696 |
---|---|
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. |
format | Online Article Text |
id | pubmed-8281810 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT gonzalezavendanomariela ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT zunigaalmonacidsimon ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT silvaian ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT lavanderosboris ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT robinsonfelipe ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT rosalesrojasroberto ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT duranverdugofabio ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT gonzalezwendy ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT caceresmonica ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT cerdaoscar ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata AT vergarajaqueariela ppimassaninteractivewebservertoidentifyproteinproteininteractionsfrommassspectrometrybasedproteomicsdata |