A global analysis of peptide fragmentation variability

Understanding the fragmentation process in MS/MS experiments is vital when trying to validate the results of such experiments, and one way of improving our understanding is to analyze existing data. We here present our findings from an analysis of a large and diverse data set of MS/MS-based peptide identifications, in which each peptide has been identified from multiple spectra, recorded on two commonly used types of electrospray instruments. By analyzing these data we were able to study fragmentation variability on three levels: (i) variation in detection rates and intensities for fragment ions from the same peptide sequence measured multiple times on a single instrument; (ii) consistency of rank-based fragmentation patterns; and (iii) a set of general observations on fragment ion occurrence in MS/MS experiments, regardless of sequence. Our results confirm that substantial variation can be found at all levels, even when high-quality identifications are used and the experimental conditions as well as the peptide sequences are kept constant. Finally, we discuss the observed variability in light of ongoing efforts to create spectral libraries and predictive software for target selection in targeted proteomics.