The peptide re-ranking code is written and tested based on ESI LC-MS/MS label-free MS data. For MALDI-like data, preprocessing (e.g. baseline correction) is needed.

The optimization problem is solved by SLEP:
http://www.public.asu.edu/~jye02/Software/SLEP/


Peptide re-ranking is carried out by running "pep_reranking.m". The parameters are specified by configuration files. The configuration files used in our experiments are available as supplementary documents at:
http://bioinformatics.ust.hk/pepreranking/

The major program is written in Matlab. Ruby is used to process text data such as X!Tandem result, protein database.