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PPC: Peak Probability Contrasts
Class Prediction Software for Protein Mass Spectometry Data

Features:

Performs sample classification from Protein Mass Spectra
via the "Peak Probability Contrasts'' method of Tibshirani, Hastie, Narasimhan, Soltys, Shi, Koong, and Le
" Sample classification from protein mass spectrometry, by peak probability contrasts" " Bioinformatics. 2004 Jun 29.

Can be applied to raw spectra, or a set of extracted peaks

Estimates prediction error via cross-validation

Provides a list of significant peaks whose intensity characterizes each diagnostic class, and estimates False Discovery Rates for these peaks.

Developed at Stanford University Labs. Free for all users.

How PPC works

Two versions:

Excel Add-in: Registration page; Manual;
PPC for the R package