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- Install a Windows-compatible distribution of Perl. The
ActivePerl distribution from ActiveState is free of charge and is
available for download from the ActiveState website ( http://
http://www.activestate.com/activeperl ).
- Download the custom PROTOMAP Perl scripts from http://
http://www.scripps.edu/cravatt/protomap/. Extract the scripts into the
top-level folder in which your sub-folders containing DTASelect
data reside. Briefl y, the purposes of the three scripts are:
(a) coverage.pl – reads each DTASelect.html fi le and stores the
sequence covered by all of the peptides for each protein in
fi les called coverg.txt in each folder.
(b) protomap.pl – must be run after running coverage.pl. This
script reads each DTAselect-fi lter.txt fi le and coverage maps
generated by coverage.pl to create a single fi le called all-
data.pmap that contains combined spectral-count and
sequence- coverage information for the entire dataset.
(c) peptographer.pl – must be run last. It takes a pmap fi le as
input and produces all of the graphical peptographs and a
web- browser interface to view them.
Fig. 2 Typical organization of DTASelect data. The only requirement is that the
DTASelect data for each gel band are stored in separate folders
Global Identifi cation of Caspase Substrates
