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OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides
[Image: see text] Hydrogen–deuterium exchange mass spectrometry (HDX/MS) is increasingly used to study the dynamics of protein conformation. Coupled to native MS, HDX can also characterize the conformations of oligonucleotides and their binding to cations, small molecules, and proteins. Data process...
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/PMC10308331/ https://www.ncbi.nlm.nih.gov/pubmed/37310448 http://dx.doi.org/10.1021/acs.analchem.3c01321 |
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author | Largy, Eric Ranz, Matthieu |
author_facet | Largy, Eric Ranz, Matthieu |
author_sort | Largy, Eric |
collection | PubMed |
description | [Image: see text] Hydrogen–deuterium exchange mass spectrometry (HDX/MS) is increasingly used to study the dynamics of protein conformation. Coupled to native MS, HDX can also characterize the conformations of oligonucleotides and their binding to cations, small molecules, and proteins. Data processing and visualization of native HDX/MS of oligonucleotides requires dedicated software solutions. OligoR is a web-browser-based application that addresses the specific needs of DNA HDX/MS and native MS experiments from raw data in an open format to visualization and export of results. Whole experiments spanning many time points can be processed in minutes for several mass-separated species. To access valuable folding dynamics information, we have developed a simple and robust approach to deconvolute bimodal isotope distributions, even when they are highly overlapping. This approach is based on modeling physically possible isotope distributions determined from chemical formulae and could be extended to any type of analyte (proteins, peptides, sugars, and small molecules). All results are presented in interactive data tables, and publication-quality figures can be generated, customized, and exported. |
format | Online Article Text |
id | pubmed-10308331 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-103083312023-06-30 OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides Largy, Eric Ranz, Matthieu Anal Chem [Image: see text] Hydrogen–deuterium exchange mass spectrometry (HDX/MS) is increasingly used to study the dynamics of protein conformation. Coupled to native MS, HDX can also characterize the conformations of oligonucleotides and their binding to cations, small molecules, and proteins. Data processing and visualization of native HDX/MS of oligonucleotides requires dedicated software solutions. OligoR is a web-browser-based application that addresses the specific needs of DNA HDX/MS and native MS experiments from raw data in an open format to visualization and export of results. Whole experiments spanning many time points can be processed in minutes for several mass-separated species. To access valuable folding dynamics information, we have developed a simple and robust approach to deconvolute bimodal isotope distributions, even when they are highly overlapping. This approach is based on modeling physically possible isotope distributions determined from chemical formulae and could be extended to any type of analyte (proteins, peptides, sugars, and small molecules). All results are presented in interactive data tables, and publication-quality figures can be generated, customized, and exported. American Chemical Society 2023-06-13 /pmc/articles/PMC10308331/ /pubmed/37310448 http://dx.doi.org/10.1021/acs.analchem.3c01321 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 | Largy, Eric Ranz, Matthieu OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides |
title | OligoR: A Native
HDX/MS Data Processing Application
Dedicated to Oligonucleotides |
title_full | OligoR: A Native
HDX/MS Data Processing Application
Dedicated to Oligonucleotides |
title_fullStr | OligoR: A Native
HDX/MS Data Processing Application
Dedicated to Oligonucleotides |
title_full_unstemmed | OligoR: A Native
HDX/MS Data Processing Application
Dedicated to Oligonucleotides |
title_short | OligoR: A Native
HDX/MS Data Processing Application
Dedicated to Oligonucleotides |
title_sort | oligor: a native
hdx/ms data processing application
dedicated to oligonucleotides |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10308331/ https://www.ncbi.nlm.nih.gov/pubmed/37310448 http://dx.doi.org/10.1021/acs.analchem.3c01321 |
work_keys_str_mv | AT largyeric oligoranativehdxmsdataprocessingapplicationdedicatedtooligonucleotides AT ranzmatthieu oligoranativehdxmsdataprocessingapplicationdedicatedtooligonucleotides |