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RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein–RNA Cross-Linking/Mass Spectrometry Data
[Image: see text] Cross-linking and mass spectrometry (XL-MS) workflows are increasingly popular techniques for generating low-resolution structural information about interacting biomolecules. xQuest is an established software package for analysis of protein–protein XL-MS data, supporting stable iso...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10563164/ https://www.ncbi.nlm.nih.gov/pubmed/37669508 http://dx.doi.org/10.1021/acs.jproteome.3c00341 |
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author | Sarnowski, Chris P. Götze, Michael Leitner, Alexander |
author_facet | Sarnowski, Chris P. Götze, Michael Leitner, Alexander |
author_sort | Sarnowski, Chris P. |
collection | PubMed |
description | [Image: see text] Cross-linking and mass spectrometry (XL-MS) workflows are increasingly popular techniques for generating low-resolution structural information about interacting biomolecules. xQuest is an established software package for analysis of protein–protein XL-MS data, supporting stable isotope-labeled cross-linking reagents. Resultant paired peaks in mass spectra aid sensitivity and specificity of data analysis. The recently developed cross-linking of isotope-labeled RNA and mass spectrometry (CLIR-MS) approach extends the XL-MS concept to protein–RNA interactions, also employing isotope-labeled cross-link (XL) species to facilitate data analysis. Data from CLIR-MS experiments are broadly compatible with core xQuest functionality, but the required analysis approach for this novel data type presents several technical challenges not optimally served by the original xQuest package. Here we introduce RNxQuest, a Python package extension for xQuest, which automates the analysis approach required for CLIR-MS data, providing bespoke, state-of-the-art processing and visualization functionality for this novel data type. Using functions included with RNxQuest, we evaluate three false discovery rate control approaches for CLIR-MS data. We demonstrate the versatility of the RNxQuest-enabled data analysis pipeline by also reanalyzing published protein–RNA XL-MS data sets that lack isotope-labeled RNA. This study demonstrates that RNxQuest provides a sensitive and specific data analysis pipeline for detection of isotope-labeled XLs in protein–RNA XL-MS experiments. |
format | Online Article Text |
id | pubmed-10563164 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-105631642023-10-11 RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein–RNA Cross-Linking/Mass Spectrometry Data Sarnowski, Chris P. Götze, Michael Leitner, Alexander J Proteome Res [Image: see text] Cross-linking and mass spectrometry (XL-MS) workflows are increasingly popular techniques for generating low-resolution structural information about interacting biomolecules. xQuest is an established software package for analysis of protein–protein XL-MS data, supporting stable isotope-labeled cross-linking reagents. Resultant paired peaks in mass spectra aid sensitivity and specificity of data analysis. The recently developed cross-linking of isotope-labeled RNA and mass spectrometry (CLIR-MS) approach extends the XL-MS concept to protein–RNA interactions, also employing isotope-labeled cross-link (XL) species to facilitate data analysis. Data from CLIR-MS experiments are broadly compatible with core xQuest functionality, but the required analysis approach for this novel data type presents several technical challenges not optimally served by the original xQuest package. Here we introduce RNxQuest, a Python package extension for xQuest, which automates the analysis approach required for CLIR-MS data, providing bespoke, state-of-the-art processing and visualization functionality for this novel data type. Using functions included with RNxQuest, we evaluate three false discovery rate control approaches for CLIR-MS data. We demonstrate the versatility of the RNxQuest-enabled data analysis pipeline by also reanalyzing published protein–RNA XL-MS data sets that lack isotope-labeled RNA. This study demonstrates that RNxQuest provides a sensitive and specific data analysis pipeline for detection of isotope-labeled XLs in protein–RNA XL-MS experiments. American Chemical Society 2023-09-05 /pmc/articles/PMC10563164/ /pubmed/37669508 http://dx.doi.org/10.1021/acs.jproteome.3c00341 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Sarnowski, Chris P. Götze, Michael Leitner, Alexander RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein–RNA Cross-Linking/Mass Spectrometry Data |
title | RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis
of Protein–RNA
Cross-Linking/Mass Spectrometry Data |
title_full | RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis
of Protein–RNA
Cross-Linking/Mass Spectrometry Data |
title_fullStr | RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis
of Protein–RNA
Cross-Linking/Mass Spectrometry Data |
title_full_unstemmed | RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis
of Protein–RNA
Cross-Linking/Mass Spectrometry Data |
title_short | RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis
of Protein–RNA
Cross-Linking/Mass Spectrometry Data |
title_sort | rnxquest: an extension to the xquest pipeline enabling analysis
of protein–rna
cross-linking/mass spectrometry data |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10563164/ https://www.ncbi.nlm.nih.gov/pubmed/37669508 http://dx.doi.org/10.1021/acs.jproteome.3c00341 |
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