Description, Instructions, and Tips for MS-Isotope


This document provides instructions for MS-Isotope.

If your web browser supports HTML5/Javascript a graph of the isotope distribution is also displayed. Server Administrators can customize the appearance of the graph by editing the sp_graph.par.txt file. If your browser has problems displaying the graph you can disable it by deselecting the Display Graph checkbox. The MS-Isotope results page will not then include graphical display of the isotope distribution.

Contents of this document:

Links to topics in the general instructions:

Introduction and Background

MS-Isotope is program for generating isotope profiles. The web version of the program allows up to six, potentially overlapping, profiles to be displayed on the same graph. The profiles can be specified as peptide sequences, elemental composition or averagine masses. The charges and intensities of the profiles must also be specified. If tab delimited text output is chosen the graph information is displayed as a table.

When used from the command line the number of profiles is unlimited.

The program can be used to simulate quantification data or entire MS/MSMS spectra.


The charge of each profile must be specified. The program can simulate multiple overlapping profiles with different charge states.


The individual profiles can have different relative intensities to, for example, simulate quantification data.

Distribution Type

You can choose to calculate the isotopic distribution of a peptide sequence, an elemental composition or an averagine mass. The peptide sequence can contain modified amino acids and have modified N and C termini.

Profile Type

This parameter defines the peak shape used when plotting the isotopic distribution.


This parameter defines the resolution used when plotting the isotopic distribution. The resolution is the full width at half maximum (FWHM).

Averagine Mass

An averagine mass gives you a typical profile that you would obtain for a given mass charge combination assuming that the peptide is made up of "average" amino acids - it is most useful for fitting profiles against unknown spectra. The elemental composition used for averagine was:

C 4.9384 H 7.7583 N 1.3577 O 1.4773 S 0.0417

(Senko et al, J Am Soc MS 1995 pp. 229-233).

Detailed Report

If the Detailed Report option is checked a table listing the individual components of each isotopic peak is given in addition to the standard report.