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chevron_left Hydrogen-deuterium exchange chevron_right
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Protocols

HDX workbench specifications

Information


Unique identifier OMICS_06891
Name HDX workbench
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Windows
Computer skills Medium
Stability Stable
Maintained Yes

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Publication for HDX workbench

HDX workbench citations

 (28)
library_books

Lipid binding promotes the open conformation and tumor suppressive activity of neurofibromin 2

2018
Nat Commun
PMCID: 5889391
PMID: 29626191
DOI: 10.1038/s41467-018-03648-4

[…] change HDX analyses were performed in triplicate, with single preparations of each protein/ligand complex. The intensity weighted mean m/z centroid value of each peptide envelope was calculated using HDX Workbench and these values were converted into percentage of deuterium incorporation. This was accomplished by determining the observed averages of the undeuterated and fully deuterated spectra an […]

library_books

Sites associated with Kalydeco binding on human Cystic Fibrosis Transmembrane Conductance Regulator revealed by Hydrogen/Deuterium Exchange

2018
Sci Rep
PMCID: 5856801
PMID: 29549268
DOI: 10.1038/s41598-018-22959-6

[…] for each on-exchange time point were obtained in 3 replicates. All HDX data were normalized to 100% D2O content, corrected for an estimated average deuterium recovery of 70%, and processed using the HDX WorkBench (version 3.3, Pascal B.D. et al., J. Am. Soc. Mass Spectrom. 2012, 23: 1512–1521). […]

library_books

Mouse and Human Monoclonal Antibodies Protect against Infection by Multiple Genotypes of Japanese Encephalitis Virus

2018
MBio
PMCID: 5829823
PMID: 29487230
DOI: 10.1128/mBio.00008-18

[…] Acquired spectra were analyzed using HDX workbench software () against a peptide set generated as described below. The deuterium level was normalized to the maximum deuterium concentration (80%) contained in the reaction vial. The peptid […]

library_books

Effects of Distal Mutations on the Structure, Dynamics and Catalysis of Human Monoacylglycerol Lipase

2018
Sci Rep
PMCID: 5789057
PMID: 29379013
DOI: 10.1038/s41598-017-19135-7

[…] e time point were obtained. From mass spectra obtained during HDX-MS experiments, the centroid of each deuterated peptide envelope and the relative deuterium uptake by each peptide were calculated by HDX WorkBench. Corrections for back exchange were made by considering the values of 80% deuterium content of the exchange buffer and an estimated 70% deuterium recovery. Paired t-tests were used to ve […]

library_books

The Sequence specific Peptide binding Activity of the Protein Sulfide Isomerase AGR2 Directs Its Stable Binding to the Oncogenic Receptor EpCAM*

2018
PMCID: 5880107
PMID: 29339412
DOI: 10.1074/mcp.RA118.000573

[…] because the EpCAMY251A mutation attenuates wt-AGR2 binding ().Another feature of the deuterated peptide data (for example, observed in supplemental Fig. S1, S3, S5, and S7) and in other studies using HDX Workbench () or HDExaminer () is that larger peptide fragments can have a different number of deuteron exchanges than predicted within smaller or partially overlapping fragments. For example, in A […]

call_split

Utilization of peptide phage display to investigate hotspots on IL 17A and what it means for drug discovery

2018
PLoS One
PMCID: 5766103
PMID: 29329326
DOI: 10.1371/journal.pone.0190850
call_split See protocol

[…] tide mixtures were separated by reversed phase liquid chromatography on an analytical C18 column and eluted into the mass spectrometer (Q-Exactive, Thermo Scientific). HDX-MS data were processed with HDX Workbench software [] […]


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HDX workbench institution(s)
Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, Jupiter, FL, USA

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