Interpretation of Collision-Induced Fragmentation Tandem Mass Spectra of Posttranslationally Modified Peptides

Tandem collision-induced dissociation (CID) mass spectrometry (MS) provides a sensitive means of analyzing the amino acid sequence of peptides. Modern MS instrumentation is capable of rapidly generating many thousands of tandem mass spectra, and protein database search engines have been developed to cope with this avalanche of data. In most studies, there is a schism between discarding perfectly valid data and including nonsensical peptide identifications—this is currently a major bottleneck in data analysis and it calls for manual evaluation of the data. Especially for posttranslationally modified peptides, there is a need for manual validation of the data because search algorithms seldom have been optimized for the identification of modified peptides and because there are many pitfalls for the unwary. This chapter describes some of the issues that should be considered when interpreting and validating low-energy CID tandem mass spectra and gives some useful tables to aid this process.