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PMID: 19135386 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

HD desktop: an integrated platform for the analysis and visualization of H/D exchange data.

Journal of the American Society for Mass Spectrometry ·Vol. 20 ·No. 4 ·2009-04-00 ·Pages 601-10

Pascal BD, Chalmers MJ, Busby SA, Griffin PR

Abstract

Here we describe an integrated software platform titled HD Desktop designed specifically to enhance the analysis of hydrogen/deuterium exchange (HDX) mass spectrometry data. HD Desktop integrates tools for data extraction with visualization components within a single web-based application. The interface design enables users to navigate from the peptide view to the sample and experiment levels, tracking all manipulations while updating the aggregate graphs in real time. HD Desktop is integrated with a relational database designed to provide performance enhancements, as well as a robust model for data storage and retrieval. Additional features of the software include retention time determination, which is achieved with the use of theoretical isotope fitting; here, we assume that the best theoretical fit will occur at the correct retention time for any given peptide. Peptide data consolidation for the rendering of data in 2D was realized by automating known and novel approaches. Designed to address broad needs of the HDX community, the platform presented here provides an efficient and manageable workflow for HDX data analysis and is freely available as a web tool at the project home page http://hdx.florida.scripps.edu.

MeSH Terms
Database Management Systems Databases as Topic Deuterium Exchange Measurement Information Storage and Retrieval/methods Internet Mass Spectrometry Peptides/analysis Proteins/analysis Software User-Computer Interface
Chemicals
Peptides Proteins
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Pascal Bruce D
Informatics, The Scripps Research Institute-Scripps Florida, Jupiter, Florida 33458, USA.
Chalmers Michael J
Busby Scott A
Griffin Patrick R
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Article Info
Journal
Journal of the American Society for Mass Spectrometry
Abbr.
J Am Soc Mass Spectrom
ISSN
1879-1123
DOI
10.1016/j.jasms.2008.11.019
Published
2009-04-00
Epub
2008-00-06
Pages
601-10
Language
English
Region
United States
NLM ID
9010412
PMCID
PMC2792908
Subset
IM
Grants
NIMH NIH HHS · U54 MH084512 · United States
NIMH NIH HHS · U54 MH084512-010010 · United States
NIGMS NIH HHS · R01 GM084041 · United States
NIMH NIH HHS · U54MH084512 · United States
NIGMS NIH HHS · R01 GM084041-02 · United States
External Links
PubMed source DOI: 10.1016/j.jasms.2008.11.019 PMC Full Text View journal details
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