Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

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) and Masson et al. (2019) . 'HDXBoxeR' citation: Janowska et al. (2024) .

HDXBoxeR

HDXBoxeR is a tool designed to streamline various aspects of HDX (Hydrogen-Deuterium Exchange) data analysis:

1. Data Reprocessing: Reprocesses data to the format required for data publication.
2. Parameter Calculation: Calculates parameters for a general HDX summary table, including backexchange, peptide lengths, and statistical information.
3. Output Conversion: Converts output from HDXExaminer (formerly Sierra Analytics, now Trajan Scientific) to a more manageable and analyzable format.
4. Statistical Analysis: Identifies peptides significantly different between sets using Welch T-tests.
5. Script Generation: Generates scripts for Pymol visualization.
6. Plot Generation: Facilitates easy plot generation, including heat maps, robot plots (modified butterfly plots), significant peptides, volcano plots, and average deuteration.
7. ExtReme Inputs: Generates inputs for ExtReme, enabling comparison between different protein states and discrimination of significantly different peptides.

Usage

HDXBoxeR can be used to enhance the efficiency and effectiveness of HDX data analysis, providing tools for data processing, analysis, and visualization.

Installation & Loading

First, ensure that you have R (and RStudio) installed on your computer. Then you can proceed with the installation of the HDXBoxeR package. There are two methods to install the HDXBoxeR package:

1. CRAN

To install, use the following command:

install.packages("HDXBoxeR") #execute only once

1. GitHub

The HDXBoxeR package is available on GitHub and can be installed using the devtools package. This method of installation is an alternative to the CRAN method.

install.packages("devtools") #if not installed

library(devtools) #run next two commends only once

devtools::install_github("mkajano/HDXBoxeR")

Loading

After installing HDXBoxeR in R, load the package using following command:

library(HDXBoxeR)

vignette and examples

Please access the vignette with examples at:

https://cran.r-project.org/web//packages/HDXBoxeR/vignettes/HDXBoxeR.html

test data location:

After HDXBoxeR package installation the test data will be located in system files of the HDXBoxeR. The path to the input table is shown below:

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")

License

This project is licensed under the GPL (>= 2) licence