Supplementary Material

Shiwei Sun, Chungong Yu, Yantao Qiao, Yu Lin, Gongjin Dong, Changning Liu, Jingfen Zhang, Zhuo Zhang, Jinjin Cai, Hong Zhang, and Dongbo Bu
Deriving the Probabilities of Water Loss and Ammonia Loss for Amino Acids from Tandem Mass Spectra
Journal of Proteome Research , 7, 202–208 (2008)

PI is a program for interpreting MS/MS data,
whose performance has been tested over three public datasets which from A8_PI, Gygi and Keller.

A8_IP	This is the experiment results on A8_IP data set, which includes the training set, the testing set and the parameters to loss a NH3 or a H2O.
PI_package	This is a PI package for download, which includes the source code package and a jar file.
Experiment_Result_On_Keller_Data	This is the experiment results on Keller's data sets.
SEQUEST_IONTRAP	This is the experiment result on the of SEQUEST runned on Gygi LTQ data.
SEQUEST_QSTAR	This is the experiment result on the of SEQUEST runned on Gygi QSTAR data.