This is a Windows, Mac and Linux console application for calculating isotope distributions for molecules. It is suitable for automation using a shell script as all parameters are specified on the command line and there is no subsequent user interaction. It is designed to work with both small molecules, proteins and other macromolecules, and can cope with most elements and isotopes. The element definitions are provided in a separate text file, which can easily be edited to allow for isotopically labelled compounds. The output is to the console by default, but can be redirected to a file, and consists of pairs of mass and abundance values.

To use the software, just download the archive, and extract the files. On MacOS X the archive should be unpacked automatically by Stuffit expander (linux users can unzip it by running the command tar -xzf isotopes.tar.gz or if that does not work try gunzip isotopes.tar.gz then tar -xf isotopes.tar). Start up the windows command prompt (under accessories on the Start Menu on XP)/ Mac console (in the utilities folder) or shell, then cd to the directory where you unpacked the files. Then run by typing:

isotopes formula

where formula is the molecular formula of interest. It currently understands "standard" elements, but not any other chemical abbreviations. Valid formulas could include C254H377N65O75S6 for insulin and C2H6O for ethanol. CH3CH2OH will work too. Parentheses are not yet supported. (On Mac and linux you need to prefix the command with ./ unless the executable file is on your path. i.e. type ./isotopes formula)

There are various other options:

isotopes formula filename.txt

The optional filename species that the program should use a different atom definition file. The file format is straigtforward, and contains the element symbol, followed by atomic number and then pairs of mass and abundance values for each isotope.

-n Normalizes the most intense peak to 100%, as is conventional for mass spectra
-f filt Normalize and only output peaks of intensity >= filt
-t thr Specifies a probability threshold thr, defaults to 0.001. Lower thresholds will find more peaks (and take longer).
-p prec Specifies the output precision prec, default is 8.
-c Outputs a comma separated table. The default is tab.

Examples:

isotopes C254H377N65O75S6      Calculates isotope distribution for insulin using default settings.

isotopes C254H377N65O75S6 -n -p 5 -c > insulin.csv    This calculates the insulin isotope distribution, outputting 5 figures of precision, normalizing the most intense peak to 100%, and sends the results to a comma separated file called insulin.csv (which will open in MS Excel if this is installed).

isotopes C254H377N65O75S6 -t 0.00001    Calculates the distribution, but will consider less likely isotopomers than with the default thr setting of 0.001

The algorithm used is based on a published procedure (J. A. Yergey, Int. J. Mass Spectrom. Ion Phys. 1983, 52, 337) but is implemented rather differently from the way described in the paper, and will not give numerically identical results.

The values for masses and abundances in the supplied file are those given by NIST.

Windows Download (isotopes.zip 200kb)

Mac OS X (PowerPC G3-G5) Download (isotopes_macPPC.tar.gz 150kb)

Linux x86 binary Download (isotopes.tar.gz 38kb)