Download PI
PI is an free package. Everybody can download PI for nonprofitable aims.
Stable version
PI_Recomb_2010_SelfAdaptiveModel_Version
PI source code package
Data Set

PI 1.3.1
source code package 
PI.jar
PI_jar_file
PI_readme.pdf Application_note_Supplement.docx
Spectrum Set
A public online spectrum set, AB_IP, from ISB was used to test our algorithm, which contains spectrum generated through shotgun analysis of proteins from human K562 cells. We restricted our analysis to doubly charged, `mobile' peptide for this proofofconcept experiment. We randomly divided the spectrum set into two parts, forming a training set containing 1803 matches, and a testing set containing 941 matches.We tested this reranking strategy on two spectrum data sets downloaded from Gygi Lab (J. E. Elias, et al,2004): one is a LTQ spectrum data set , and the other a Q_STAR spectrum data set . We used the first 2000 pairs to train our EM model, and use the second half as testing set (2011 pairs, 668 of them have been labeled falsepositive by the reversedatabase technique). Similarly, in the 5998 peptidespectrum pairs reported by Mascot for the Q_STAR data set, we chose the first half (2000 pairs) as training set, and the second half as testing set (3998 pairs, 291 of them have been labeled as false positive).