all_summary

Returns summary data.
Function returns: Protein states, timepoints, number of replicates, # peptides, % coveregae, average peptide length and redundancy.
backexchange calculations (average and range), Critical interval and standard deviation.
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

all_summary 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>replicates</dt>
<dd>number of replicates. Default set to 3.</dd>
<dt>Dfact</dt>
<dd>Dfact is the fraction of D/H in the labeling buffer used. Default set up to 0.85</dd></dl>

Arguments

Returns full summary table. — all_summary

<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>replicates</dt>
<dd>number of replicates. Default set to 3.</dd>


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

</dl>

all_summary: Returns full summary table.

Description

Usage

Value

Arguments

Examples