Literature DB >> 22692830

HDX workbench: software for the analysis of H/D exchange MS data.

Bruce D Pascal1, Scooter Willis, Janelle L Lauer, Rachelle R Landgraf, Graham M West, David Marciano, Scott Novick, Devrishi Goswami, Michael J Chalmers, Patrick R Griffin.   

Abstract

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu .

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Year:  2012        PMID： 22692830      PMCID： PMC3808162          DOI： 10.1007/s13361-012-0419-6

Source DB:  PubMed          Journal:  J Am Soc Mass Spectrom        ISSN： 1044-0305            Impact factor:   3.109


  30 in total

1.  Isotopic compositions and accurate masses of single isotopic peaks.

Authors:  Alan L Rockwood; Jordan R Van Orman; David V Dearden
Journal:  J Am Soc Mass Spectrom       Date:  2004-01       Impact factor: 3.109

2.  Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis.

Authors:  David D Weis; Thomas E Wales; John R Engen; Matthew Hotchko; Lynn F Ten Eyck
Journal:  J Am Soc Mass Spectrom       Date:  2006-07-27       Impact factor: 3.109

3.  Efficient calculation of accurate masses of isotopic peaks.

Authors:  Alan L Rockwood; Perttu Haimi
Journal:  J Am Soc Mass Spectrom       Date:  2006-02-03       Impact factor: 3.109

4.  Semi-automated data processing of hydrogen exchange mass spectra using HX-Express.

Authors:  David D Weis; John R Engen; Ignatius J Kass
Journal:  J Am Soc Mass Spectrom       Date:  2006-08-22       Impact factor: 3.109

5.  The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies.

Authors:  Damian Houde; Steven A Berkowitz; John R Engen
Journal:  J Pharm Sci       Date:  2010-12-29       Impact factor: 3.534

6.  Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments.

Authors:  Matthew Hotchko; Ganesh S Anand; Elizabeth A Komives; Lynn F Ten Eyck
Journal:  Protein Sci       Date:  2006-03       Impact factor: 6.725

7.  Distinct interaction modes of an AKAP bound to two regulatory subunit isoforms of protein kinase A revealed by amide hydrogen/deuterium exchange.

Authors:  Lora L Burns-Hamuro; Yoshitomo Hamuro; Jack S Kim; Paul Sigala; Rosa Fayos; David D Stranz; Patricia A Jennings; Susan S Taylor; Virgil L Woods
Journal:  Protein Sci       Date:  2005-10-31       Impact factor: 6.725

8.  Specificity of immobilized porcine pepsin in H/D exchange compatible conditions.

Authors:  Yoshitomo Hamuro; Stephen J Coales; Kathleen S Molnar; Steven J Tuske; Jeffrey A Morrow
Journal:  Rapid Commun Mass Spectrom       Date:  2008-04       Impact factor: 2.419

9.  Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses.

Authors:  Gordon W Slysz; Charles A H Baker; Benjamin M Bozsa; Anthony Dang; Andrew J Percy; Melissa Bennett; David C Schriemer
Journal:  BMC Bioinformatics       Date:  2009-05-27       Impact factor: 3.169

10.  The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data.

Authors:  B D Pascal; M J Chalmers; S A Busby; C C Mader; M R Southern; N F Tsinoremas; P R Griffin
Journal:  BMC Bioinformatics       Date:  2007-05-16       Impact factor: 3.169
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  144 in total

1.  Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications.

Authors:  Bruce D Pascal; Graham M West; Catherina Scharager-Tapia; Ricardo Flefil; Tina Moroni; Pablo Martinez-Acedo; Patrick R Griffin; Anthony C Carvalloza
Journal:  J Am Soc Mass Spectrom       Date:  2015-08-12       Impact factor: 3.109

2.  Identification and function of conformational dynamics in the multidomain GTPase dynamin.

Authors:  Saipraveen Srinivasan; Venkatasubramanian Dharmarajan; Dana Kim Reed; Patrick R Griffin; Sandra L Schmid
Journal:  EMBO J       Date:  2016-01-18       Impact factor: 11.598

3.  Conformational Assessment of Adnectin and Adnectin-Drug Conjugate by Hydrogen/Deuterium Exchange Mass Spectrometry.

Authors:  Richard Y-C Huang; Steven R O'Neil; Daša Lipovšek; Guodong Chen
Journal:  J Am Soc Mass Spectrom       Date:  2018-05-07       Impact factor: 3.109

4.  Integration of G protein α (Gα) signaling by the regulator of G protein signaling 14 (RGS14).

Authors:  Nicole E Brown; Devrishi Goswami; Mary Rose Branch; Suneela Ramineni; Eric A Ortlund; Patrick R Griffin; John R Hepler
Journal:  J Biol Chem       Date:  2015-02-09       Impact factor: 5.157

5.  Time window expansion for HDX analysis of an intrinsically disordered protein.

Authors:  Devrishi Goswami; Srikripa Devarakonda; Michael J Chalmers; Bruce D Pascal; Bruce M Spiegelman; Patrick R Griffin
Journal:  J Am Soc Mass Spectrom       Date:  2013-07-25       Impact factor: 3.109

6.  Resolving isotopic fine structure to detect and quantify natural abundance- and hydrogen/deuterium exchange-derived isotopomers.

Authors:  Qian Liu; Michael L Easterling; Jeffrey N Agar
Journal:  Anal Chem       Date:  2013-12-20       Impact factor: 6.986

7.  Differential isotopic enrichment to facilitate characterization of asymmetric multimeric proteins using hydrogen/deuterium exchange mass spectrometry.

Authors:  Devrishi Goswami; Steve Tuske; Bruce D Pascal; Joseph D Bauman; Disha Patel; Eddy Arnold; Patrick R Griffin
Journal:  Anal Chem       Date:  2015-03-25       Impact factor: 6.986

8.  Crystal Structures of the Nuclear Receptor, Liver Receptor Homolog 1, Bound to Synthetic Agonists.

Authors:  Suzanne G Mays; C Denise Okafor; Richard J Whitby; Devrishi Goswami; Józef Stec; Autumn R Flynn; Michael C Dugan; Nathan T Jui; Patrick R Griffin; Eric A Ortlund
Journal:  J Biol Chem       Date:  2016-09-30       Impact factor: 5.157

9.  Characterization of Aggregation Propensity of a Human Fc-Fusion Protein Therapeutic by Hydrogen/Deuterium Exchange Mass Spectrometry.

Authors:  Richard Y-C Huang; Roxana E Iacob; Stanley R Krystek; Mi Jin; Hui Wei; Li Tao; Tapan K Das; Adrienne A Tymiak; John R Engen; Guodong Chen
Journal:  J Am Soc Mass Spectrom       Date:  2016-08-15       Impact factor: 3.109

10.  Chemical Crosslinking Mass Spectrometry Reveals the Conformational Landscape of the Activation Helix of PPARγ; a Model for Ligand-Dependent Antagonism.

Authors:  Jie Zheng; Cesar Corzo; Mi Ra Chang; Jinsai Shang; Vinh Q Lam; Richard Brust; Anne-Laure Blayo; John B Bruning; Theodore M Kamenecka; Douglas J Kojetin; Patrick R Griffin
Journal:  Structure       Date:  2018-08-23       Impact factor: 5.006
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