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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 proof-of-concept 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 re-ranking 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 false-positive by the reverse-database technique). Similarly, in the 5998 peptide-spectrum 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).