Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry

Toward Standardizing Deuterium Content Reporting in Hydrogen Exchange-MS

(2014) Joey G. Sheff et al.   ANALYTICAL CHEMISTRY

Applications of Hydrogen/Deuterium Exchange MS from 2012 to 2014

(2014) Gregory F. Pirrone et al.   ANALYTICAL CHEMISTRY

QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure

(2014) Joseph P Salisbury et al.   BMC BIOINFORMATICS

Mapping Residual Structure in Intrinsically Disordered Proteins at Residue Resolution Using Millisecond Hydrogen/Deuterium Exchange and Residue Averaging

(2014) Theodore R. Keppel et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Combining Ion Mobility Spectrometry with Hydrogen-Deuterium Exchange and Top-Down MS for Peptide Ion Structure Analysis

(2014) Mahdiar Khakinejad et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation

(2014) Robert Lindner et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Mass Spec Studio for Integrative Structural Biology

(2014) Martial Rey et al.   STRUCTURE

Resolving Isotopic Fine Structure to Detect and Quantify Natural Abundance- and Hydrogen/Deuterium Exchange-Derived Isotopomers

(2013) Qian Liu et al.   ANALYTICAL CHEMISTRY

H/D Exchange Centroid Monitoring is Insufficient to Show Differences in the Behavior of Protein States

(2013) Jun Zhang et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Feature Based Retention Time Alignment for Improved HDX MS Analysis

(2013) John D. Venable et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Peptide–Column Interactions and Their Influence on Back Exchange Rates in Hydrogen/Deuterium Exchange-MS

(2013) Joey G. Sheff et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Analysis of Overlapped and Noisy Hydrogen/Deuterium Exchange Mass Spectra

(2013) Miklos Guttman et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis

(2013) Z.-Y. Kan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry—A review

(2012) Andrew J. Percy et al.   ANALYTICA CHIMICA ACTA

Site-Specific Analysis of Gas-Phase Hydrogen/Deuterium Exchange of Peptides and Proteins by Electron Transfer Dissociation

(2012) Kasper D. Rand et al.   ANALYTICAL CHEMISTRY

Improved Protein Hydrogen/Deuterium Exchange Mass Spectrometry Platform with Fully Automated Data Processing

(2012) Zhongqi Zhang et al.   ANALYTICAL CHEMISTRY

Biological insights from hydrogen exchange mass spectrometry

(2012) Sheila S. Jaswal   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Retention Time Alignment of LC/MS Data by a Divide-and-Conquer Algorithm

(2012) Zhongqi Zhang   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Hydrogen Exchange Mass Spectrometry: Are We Out of the Quicksand?

(2012) Roxana E. Iacob et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Improved Sequence Resolution by Global Analysis of Overlapped Peptides in Hydrogen/Deuterium Exchange Mass Spectrometry

(2012) Piotr G. Fajer et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Using Hydrogen/Deuterium Exchange Mass Spectrometry to Study Conformational Changes in Granulocyte Colony Stimulating Factor upon PEGylation

(2012) Hui Wei et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

HDX Workbench: Software for the Analysis of H/D Exchange MS Data

(2012) Bruce D. Pascal et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Charged linker sequence modulates eukaryotic heat shock protein 90 (Hsp90) chaperone activity

(2012) S. Tsutsumi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prediction of Collision-Induced-Dissociation Spectra of Peptides with Post-translational or Process-Induced Modifications

(2011) Zhongqi Zhang   ANALYTICAL CHEMISTRY

HDX-Analyzer: a novel package for statistical analysis of protein structure dynamics

(2011) Sanmin Liu et al.   BMC BIOINFORMATICS

Differential hydrogen/deuterium exchange mass spectrometry analysis of protein–ligand interactions

(2011) Michael J Chalmers et al.   Expert Review of Proteomics

Cross-Monomer Substrate Contacts Reposition the Hsp90 N-Terminal Domain and Prime the Chaperone Activity

(2011) Timothy O. Street et al.   JOURNAL OF MOLECULAR BIOLOGY

HDXFinder: Automated Analysis and Data Reporting of Deuterium/Hydrogen Exchange Mass Spectrometry

(2011) Danny E. Miller et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

ETD in a Traveling Wave Ion Guide at Tuned Z-Spray Ion Source Conditions Allows for Site-Specific Hydrogen/Deuterium Exchange Measurements

(2011) Kasper D. Rand et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

ExMS: Data Analysis for HX-MS Experiments

(2011) Zhong-Yuan Kan et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Quantitative Assessment of Protein Structural Models by Comparison of H/D Exchange MS Data with Exchange Behavior Accurately Predicted by DXCOREX

(2011) Tong Liu et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Evidence for Increased Exposure of the Notch1 Metalloprotease Cleavage Site upon Conversion to an Activated Conformation

(2011) Kittichoat Tiyanont et al.   STRUCTURE

Hydrogen exchange mass spectrometry: what is it and what can it tell us?

(2010) Sean R. Marcsisin et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Prediction of Electron-Transfer/Capture Dissociation Spectra of Peptides

(2010) Zhongqi Zhang   ANALYTICAL CHEMISTRY

Deuteration distribution estimation with improved sequence coverage for HX/MS experiments

(2010) Xinghua Lou et al.   BIOINFORMATICS

Simultaneous and selective inference: Current successes and future challenges

(2010) Yoav Benjamini   BIOMETRICAL JOURNAL

Computing H/D-Exchange rates of single residues from data of proteolytic fragments

(2010) Ernst Althaus et al.   BMC BIOINFORMATICS

Hydrogen exchange mass spectrometry for studying protein structure and dynamics

(2010) Lars Konermann et al.   CHEMICAL SOCIETY REVIEWS

Methods for the analysis of high precision differential hydrogen–deuterium exchange data

(2010) Michael J. Chalmers et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Automated detection and analysis of bimodal isotope peak distributions in H/D exchange mass spectrometry using HeXicon

(2010) Anna Kreshuk et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Investigation of amide hydrogen back-exchange in Asp and His repeats measured by hydrogen (1H/2H) exchange mass spectrometry

(2010) Kasper D. Rand et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

MSTools—Web based application for visualization and presentation of HXMS data

(2010) Daniel Kavan et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

The Utility of Hydrogen/Deuterium Exchange Mass Spectrometry in Biopharmaceutical Comparability Studies

(2010) Damian Houde et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution fourier transform ion cyclotron resonance mass spectrometry

(2010) Sasa Kazazic et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Gas-phase H/D-exchange experiments in supramolecular chemistry

(2010) Henrik D. F. Winkler et al.   NEW JOURNAL OF CHEMISTRY

Determination of amide hydrogen exchange by mass spectrometry: A new tool for protein structure elucidation

(2010) Zhongqi Zhang et al.   PROTEIN SCIENCE

H/D Exchange and Mass Spectrometry in the Studies of Protein Conformation and Dynamics: Is There a Need for a Top-Down Approach?

(2009) Igor A. Kaltashov et al.   ANALYTICAL CHEMISTRY

Protein Hydrogen Exchange Measured at Single-Residue Resolution by Electron Transfer Dissociation Mass Spectrometry

(2009) Kasper D. Rand et al.   ANALYTICAL CHEMISTRY

Large-Scale Identification and Quantification of Covalent Modifications in Therapeutic Proteins

(2009) Zhongqi Zhang   ANALYTICAL CHEMISTRY

Analysis of Protein Conformation and Dynamics by Hydrogen/Deuterium Exchange MS

(2009) John R. Engen   ANALYTICAL CHEMISTRY

NITPICK: peak identification for mass spectrometry data

(2009) Bernhard Y Renard et al.   BMC BIOINFORMATICS

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

(2009) Gordon W Slysz et al.   BMC BIOINFORMATICS

Analysis of Conformational Changes during Activation of Protein Kinase Pak2 by Amide Hydrogen/Deuterium Exchange

(2008) Yuan-Hao Hsu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein structure and dynamics studied by mass spectrometry: H/D exchange, hydroxyl radical labeling, and related approaches

(2008) Lars Konermann et al.   JOURNAL OF MASS SPECTROMETRY

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

(2008) Bruce D. Pascal et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Assessment of the repeatability and reproducibility of hydrogen/deuterium exchange mass spectrometry measurements

(2008) William Burkitt et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

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

(2008) Yoshitomo Hamuro et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY