Added a new word document with Jarrett's changes to the manuscript.  This
is kind of like a "brach" on just the document for now rather than
branching the whole project.
Added ProteasomeFigure directory under figures, which contains code to
run an MSStats analysis on the intial Skyline reports.  Also, under
PeptideLevel is a script to make plots of the individual peptide response
to rapamycin.  The code under MSStats requires MSStats v 1.99beta to be
installed as well as R.  It's not really meant to be run by anyone except
Jarrett on his local machine for the time being.
Cleaned up the ProteasomeFigure directory
Added README documents in the figures/ProteasomeFigure sub directory