Draw H/D Exchange Plots

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Contents

• Tool description
• Input fields
  • Digest file
  • Use colors
  • Show minor X marks
  • Lowest/Highest Y value
  • Step of Y values
  • Lowest/Highest X value
  • Logarithmic X axis
  • Draw lines
• Tips and examples

Tool description

This utility draws the H/D exchange graphs for multiple peptides. It plots percentage of deuteration (or number of deuterons) versus time. It can handle up to eight different experimental conditions in one graph. It is possible to use logarithmic or linear scale on the x-axis and it supports user defined limits on the y-axis.

If you are using MS Tools use this citation in your papers please:
Kavan, D. and Man, P. "MSTools - Web based application for visualization and presentation of HXMS data" Int. J. Mass Spectrom. 2011, 302: 53-58. http://dx.doi.org/10.1016/j.ijms.2010.07.030.
You can also include the actual link to MSTools: http://peterslab.org/MSTools/

Input fields

Digest file

This text file contains information about peptides and their deuteration (expressed in % or as number of deuterons) at different times and under various conditions. First line must contain the headers (first three columns) From, To and Time. All times must be converted to seconds. Next columns are reserved for individual conditions and their description is placed on the first line. The lines bellow header are reserved for the actual data, each line must contain peptide limits, time and percentage of deuteration at the respective time point. Lines not containing appropriate number of columns (and numbers in them) are ignored, so you can leave empty lines between peptides or insert some comment line. All columns have to be separated by a tab.

You can download an example digest file.

Use colors

This check box toggles the use of colors in the graphs. If this box is unchecked, data series will differ just in symbols.

Show minor X marks

This check box toggles the use of minor marks on the x-axis.

Lowest/Highest Y value

These two input fields set the y-axis limits. Minimal accepted value is 0, maximal accepted value is 100, as it is designed primarily for percentage values. However it can accept the number of deuterons as well if the plots are drawn for peptides obtained after proteolysis (these can hardly exceed 100). If the entered values are incorrect (e.g. the Highest is lower than the Lowest) these values default to 0 and 100.

Step of Y values

The interval between two numbers describing y-axis.

Lowest/Highest X value

These two input fields set the x-axis limits. Minimal accepted value is 0. If the logarithmic scale is set, the minimal value is 1. If the Highest value is lower than the Lowest, it is set as from 10 to 100,000.

Logarithmic X axis

`This checkbox toggles the use of logarithmic and linear scale of the x-axis.

Draw lines

This field switches the data points connecting lines on and off.

Tips and examples

The result files are in svg format and thus can be edited in any vector graphic editor that can handle the format. If you just want to convert it into a bitmap, you can use one of several convertors (Batik SVG Toolkit). Alternatively you can use online converters, e.g. svg2raster. You can also print it immediately from the web browser.