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 in publications

 (27)
PMCID: 5889391
PMID: 29626191
DOI: 10.1038/s41467-018-03648-4

[…] 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 […]

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)., the datasets generated during and/or analysed during the current study are available […]

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

[…] system was kept in an ice bath, except for the pepsin column, to minimize back exchange. duplicate measurements were carried out for each of the time points., 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. […]

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

[…] 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 […]

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

[…] 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, […]


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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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