Supplementary Material

Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang, Xiaofei Liu, Chungong Yu, Dongbo Bu, Runsheng Chen
A novel scoring schema for identification by searching protein sequence databases using tandem mass spectrometry data
BMC Bioinformatics, 7, 222 (2006)

PI is a program for interpreting MS/MS data (database searching),
whose performance has been tested over two public datasets--- "Mix" and "OPD_08".

PI_0.5.c	This is the source code of our program.
probability.cfg	This the probability of characteristic ions and noise.
trypsin.cfg	Enzymatic site of trypsin
mix.protein.db	Protein database of for searching, human proteins (false) together with the mixture proteins(ture).
mix_data.tar.gz	MS/MS data of the mixture.
mix.training.protein.db.1	Protein database 1 in the mixture for training parameters.
mix.training.assignment.1	The training set 1 in the mixture.
mix.testing.protein.db.1	Protein database in the mixture searched by PI in the first round of testing its performance.
mix.assignment.PI+.1	Positive assignments by using PI to search mix.testing.protein.db.1.
mix.assignment.SEQ+.1	Positive assignments by using SEQUEST to search mix.testing.protein.db.1.
mix.assignment.PI+SEQ-.manual_inspection.1	The assignments found by PI but not by SEQUEST. These assignments have been manually inspected.
mix.training.protein.db.2	Protein database 2 in the mixture for training parameters.
mix.training.assignment.2	The training set 2 in the mixture.
mix.testing.protein.db.2	Protein database in the mixture searched by PI in the second round of testing its performance.
mix.assignment.PI+.2	Positive assignments by using PI to search mix.testing.protein.db.2
mix.assignment.SEQ+.2	Positive assignments by using SEQUEST to search mix.testing.protein.db.2
mix.assignment.PI+SEQ-.manual_inspection.2	The assignments found by PI but not by SEQUEST. These assignments have been manually inspected.
mix.training.protein.db.3	Protein database.3 in the mixture for training parameters.
mix.training.assignment.3	The training set.3 in the mixture.
mix.testing.protein.db.3	Protein database in the mixture searched by PI in the third round of testing its performance.
mix.assignment.PI+.3	Positive assignments by using PI to search mix.testing.protein.db.3.
mix.assignment.SEQ+.3	Positive assignments by using SEQUEST to search mix.testing.protein.db.3.
mix.assignment.PI+SEQ-.manual_inspection.3	The assignments found by PI but not by SEQUEST. These assignments have been manually inspected.
mix.result.summary	The summary of performance of PI.
OPD_08.protein.db	protein database of for searching, predicted proteins from Mycobacterium_smegmatis together with the corrected peptide set.
OPD_08.assignment.PI+	Positive assignments by PI.
OPD_08.assignment.SEQ+	Positive assignments by SEQUEST.
OPD_08.assignment.PI+SEQ-.full	Assignments found by PI but not found by SEQUEST. These assignments have not been manually inspected.
OPD_08.assignment.PI+SEQ-.partial	One tenth of assignments in "OPD_08.assignment.PI+SEQ-.full" was sampled to be manually inspected.
OPD_08.assignment.PI+SEQ-.manual_inspection	Assignments in "OPD_08.assignment.PI+SEQ-.partial" that were positive by manually inspection.
OPD_08.result.summary	Summary of PI performance over the OPD_08.