Anal. Chem. 2006, 78, 1921-1929
Cross-Correlation Algorithm for Calculation of Peptide Molecular Weight from Tandem Mass Spectra John D. Venable, Tao Xu, Daniel Cociorva, and John R. Yates III*
Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
We have developed an approach to identify the molecular weight of a peptide ion directly from its corresponding tandem mass spectrum using a cross-correlation function. We have shown that the monoisotopic molecular weight can be calculated for ∼90% of tandem mass spectra identified from tryptic digests of complex protein mixtures. The accuracy of the calculated monoisotopic masses was dependent on the resolution and mass accuracy of the spectra analyzed, but was typically 2 are difficult to resolve. In addition, good quality tandem (1) Eng, J. K.; McCormack, A. L.; Yates, J. R., III. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989. (2) Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Electrophoresis 1999, 20, 3551-3567. (3) Sadygov, R. G.; Yates, J. R., I. Anal. Chem. 2003, 75, 3792-3798. 10.1021/ac051636h CCC: $33.50 Published on Web 02/09/2006
© 2006 American Chemical Society
mass spectra can often be acquired and identified from signals that are barely detectable in normal MS mode operation in which the MS mode typically suffers from chemical noise. Even when using high-performance mass spectrometers (i.e., LTQ-FTMS, LTQ-Orbitrap, Q-TOF), accurately measuring the molecular weights of precursor ions from these low-abundance peptides can be difficult. Moreover, the accuracy of any mass spectrometry measurement is dependent on the intensity of the signal, with larger signals typically being much more accurate. In our lab, we routinely identify peptides from precursor ions (in the MS scan) with signal-to-noise ratios
