Cross-Correlation Algorithm for Calculation of Peptide Molecular Weight from Tandem Mass Spectra

• Published in: Analytical chemistry (Washington) Vol. 78; no. 6; pp. 1921 - 1929
• Main Authors: Venable, John D, Xu, Tao, Cociorva, Daniel, Yates, John R
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 15.03.2006
• Subjects: Algorithms; Analytical chemistry; Chemistry; Exact sciences and technology; Mass spectrometry; Molecular Weight; Peptides; Peptides - chemistry; Sensitivity and Specificity; Software; Spectrometric and optical methods; Tandem Mass Spectrometry - methods; Performance evaluation; Peptides; Low resolution; Algorithm; Precursor; Protein; Ion trap; Accuracy; Cross correlation; Database; Correlation function; Dissociation; Molecular mass; Mass spectrometry
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/ac051636h

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 <0.25 amu for linear ion trap mass spectra. The ability to calculate accurate monoisotopic molecular weights for low-resolution ion trap data should significantly improve both the speed and performance of database searches for which typical mass accuracies of ∼3 amu are employed. In addition, this strategy can also be used to identify the precursor ion for tandem mass spectra acquired using large ion selection windows in data-independent collision-activated dissociation and has the potential to identify multiplexed tandem mass spectra.