cd TPP-x.x.x/trans_proteomic_pipeline/src/Search/SpectraST make -f Makefile_STANDALONE_LINUX
If you have some problems with dependencies this tips should help:
I successfully installed the standalone version of SpectraST on an Ubuntu machine, but I had to make the two following changes. Perhaps these changes could be made to the prerequisites script and the source, respectively. Details below.
1. install libgsl0-dev from apt-get
2. modify SpectraST_util.cpp to include unistd.h
As for the first, I understand that the prerequisites scripts don't include Ubuntu 13.04. Perhaps the second issue is also specific to later ubuntu versions.
Ubuntu 13.04, 64-bit
1. gsl dependency
$ cd TPP-4.6.3/trans_proteomic_pipeline/src/Search/SpectraST