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General Usage Notes

isodist isodist_parameters.in

If isodist is installed into /usr/local/bin, you invoke the program with a command similar to the above, specifying a parameter file. If it is installed elsewhere, you may need to explicitly specify the path to the executable

isodist requires 4 files in addition to the executable, as well as data files to process. All of these files may have any name.

1. A parameter file, which sets certain configuration options, and provides the locations of the other 3 files (isodist_parameters.in in the above example)
2. An atom definitions file, which specifies all of the available atom types
3. A residue and model definitions file, which defines all of the available residues, as well as the species whose distributions you will calculate
4. A batch file which supplies a list of data files which will be fit based on the supplied model file as well as sequence and charge information

Output

For each data file listed in the batchfile, isodist will create two output files in the same directory.

1. A .dat file, which is the original data file, converted from M/Z to the Mass domain. When the charge is 1, the data should be unchanged
2. A .fit file, which is a series of (Mass, Intensity) points representing the best fit calculated spectrum as generated by isodist

Additionally, a csv file (comma separate values) will be generated containing a summary of the batch process, including fitted parameters for each of the peptides, such as amplitude and extent of labeling.

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