title: HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry.
abstract: Hydrogen/deuterium exchange in combination with mass spectrometry (H/D MS) is a sensitive technique for detection of changes in protein conformation and dynamics. However, wide application of H/D MS has been hindered, in part, by the lack of computational tools necessary for efficient analysis of the large data sets associated with this technique. We report a novel web-based application for automatic analysis of H/D MS experimental data. This application relies on the high resolution of mass spectrometers to extract all isotopic envelopes before correlating these envelopes with individual peptides. Although a fully automatic analysis is possible, a variety of graphical tools are included to aid in the verification of correlations and rankings of the isotopic peptide envelopes. As a demonstration, the rate constants for H/D exchange of peptides from rabbit muscle pyruvate kinase are mapped onto the structure of this protein.
authors.affiliation: Biochemistry and Molecular Biology, The University of Kansas Medical Center, MS 3030, 3901 Rainbow Blvd., Kansas City, KS 66160, USA.
authors.forename: Danny E
authors.initials: DE
authors.lastname: Miller
authors.forename: Charulata B
authors.initials: CB
authors.lastname: Prasannan
authors.forename: Maria T
authors.initials: MT
authors.lastname: Villar
authors.forename: Aron W
authors.initials: AW
authors.lastname: Fenton
authors.forename: Antonio
authors.initials: A
authors.lastname: Artigues
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D041961:Deuterium Exchange Measurement / Q000379:methods*; D020407:Internet; D013058:Mass Spectrometry / Q000379:methods*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011770:Pyruvate Kinase / Q000737:chemistry / Q000378:metabolism; D011817:Rabbits; D012984:Software; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D010455:Peptides; D011770:Pyruvate Kinase
references.citation: BMC Bioinformatics. 2008 Sep 20;9:387
references.pmid: 18803853
references.citation: J Am Soc Mass Spectrom. 2006 Dec;17(12):1700-3
references.pmid: 16931036
references.citation: Methods Mol Biol. 2010;604:319-31
references.pmid: 20013381
references.citation: J Biomol Tech. 2007 Sep;18(4):194-204
references.pmid: 17916792
references.citation: BMC Bioinformatics. 2010 Aug 11;11:424
references.pmid: 20701784
references.citation: J Am Soc Mass Spectrom. 2010 Apr;21(4):550-8
references.pmid: 20116280
references.citation: BMC Bioinformatics. 2007 May 16;8:156
references.pmid: 17506883
references.citation: Protein Sci. 2006 Mar;15(3):583-601
references.pmid: 16501228
references.citation: Nat Biotechnol. 2004 Nov;22(11):1459-66
references.pmid: 15529173
references.citation: J Am Soc Mass Spectrom. 2009 Mar;20(3):520-4
references.pmid: 19095461
references.citation: Proteomics. 2010 Mar;10(6):1150-9
references.pmid: 20101611
references.citation: Bioinformatics. 2010 Jun 15;26(12):1535-41
references.pmid: 20439256
references.citation: BMC Bioinformatics. 2009 May 27;10:162
references.pmid: 19473537
references.citation: Anal Chem. 2006 Feb 15;78(4):1005-14
references.pmid: 16478090
references.citation: Anal Biochem. 2003 Mar 1;314(1):46-53
references.pmid: 12633601
references.citation: J Am Soc Mass Spectrom. 2009 Apr;20(4):601-10
references.pmid: 19135386