backHX_calculations

Returns average and ranges of backexchange. Function calculates as: 1- (m100%-m0%)/N/Dfact.
m0% is the non-deuterated peptide centroid mass, m100% is the maximally labeled peptide centroid mass, N is
the theoretical number of backbone amides in the peptide and Dfrac is the fraction of D/H in the labeling buffer used.
Function requires undeuterated and Fully deuterated sets marked in Deut.time as 0s and FD respectively.

A protocol that facilitates the processing and analysis of Hydrogen-Deuterium Exchange Mass Spectrometry data using p-value statistics and Critical Interval analysis.
It provides a pipeline for analyzing data from 'HDXExaminer' (Sierra Analytics, Trajan Scientific),
automating matching and comparison of protein states through Welch's T-test and the Critical Interval statistical framework.
Additionally, it simplifies data export, generates 'PyMol' scripts, and ensures calculations meet publication standards.
'HDXBoxeR' assists in various aspects of hydrogen-deuterium exchange data analysis, including reprocessing data, calculating parameters, identifying significant peptides,
generating plots, and facilitating comparison between protein states.
For details check papers by Hageman and Weis (2019) <doi:10.1021/acs.analchem.9b01325>
and Masson et al. (2019) <doi:10.1038/s41592-019-0459-y>.
'HDXBoxeR' citation: Janowska et al. (2024) <doi:10.1093/bioinformatics/btae479>.

Maria K. Janowska

HDXBoxeR

Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

Katherine Reiter

Pearl Magala

Miklos Guttman

Rachel E. Klevit

backHX_calculations function

<dl><dt>filepath</dt>
<dd>filepath to the input file. Input file is All_results table from HDX_Examiner, where all the fields are marked for export.</dd>
<dt>Dfact</dt>
<dd>is the fraction of D/H in the labeling buffer used. Default set up to 0.85</dd></dl>

Arguments

Summary of backexchange summary — backHX_calculations

<dl>

<dt>filepath</dt>
<dd>filepath to the input file. Input file is All_results table from HDX_Examiner, where all the fields are marked for export.</dd>


<dt>Dfact</dt>
<dd>is the fraction of D/H in the labeling buffer used. Default set up to 0.85</dd>

</dl>

backHX_calculations: Summary of backexchange summary

Description

Usage

Value

Arguments

Examples