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correlation.pl
This Perl script calculates the correlation between the natural logarithms of ion abundances for two tandem mass spectra. It calculates the correlation for the y-ions and b-ions seperatly.

Run this program by writing
perl correlation.pl [sequence] [accuracy] [tandem mass spectra 1] [tandem mass spectra 2] [output file]
in the command promt
ex.
perl correlation YGGFM 0.5 msms1.dta msms2.dta result.txt

In order for this program to work the msms fils need to be in a format looking like this:
mass intensity
mass intensity
mass intensity
and so on...