METHOD TO COMPARE COLLISION-INDUCED DISSOCIATION SPECTRA OF PEPTIDES - POTENTIAL FOR LIBRARY SEARCHING AND SUBTRACTIVE ANALYSIS

We report the development of a method to compare collision-induced dis sociation (CID) spectra of peptides. This method employs a cross-corre lation analysis of a CID spectrum to a reference spectrum and normaliz es the cross-correlation score to the autocorrelation of the CID spect ra. The query spectrum is compared by using both mass information and fragmentation patterns. Fragmentation patterns are compared to each ot her using a correlation function. To evaluate the specificity of the a pproach, a set of 2180 tandem mass spectra obtained from both triple-q uadrupole tandem mass spectrometers (TSQ) and quadrupole ion trap mass spectrometers (LCQ) was created. Comparisons are performed between ta ndem mass spectra obtained on the same instrument type as well as betw een different instrument types. Accurate and reliable comparisons are demonstrated in both types of analyses. The scores obtained in the cro ss-comparison of TSQ and LCQ tandem mass spectra of the same peptide a re found to be slightly lower than comparisons performed with spectra obtained on the same instrument type. The method appears insensitive t o variations in day-to-day performance of the instrument, minor variat ions in fragment ion abundance, and instrumental differences inherent in the same instrument model. The use of this method of comparison is demonstrated for library searching and subtractive analysis of tandem mass spectra obtained during LC/MS/MS experiments.