An alternative sampling algorithm for use in liquid chromatography/tandem mass spectrometry experiments

In liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses of complex peptide mixtures, dynamic exclusion functions are used to minimize repeat selections of identical precursors for collision induced dissociation (CID). We describe a new algorithm for the dynamic exclusion of m/z values during LC/MS/MS. Full-scan based peak exclusion (Fulspec) uses a simplified model of chromatographic peak formation to detect and exclude contaminants present throughout the run or that lead to broad peaks. Therefore, instead of excluding peptides from fragment analysis according to a rigidly predefined time window, the chromatographic properties of the detected analytes are used. The algorithm was tested on two datasets derived from previously published experiments. Fulspec achieves a distribution of CID spectra with minimal tailing on the retention time axis, without resorting to rigid exclusion of m/z values. The procedure further excludes intensities with a bias towards low-quality CID spectra. This combination frees up valuable analytical capacity. The underlying intensity vs. quality analyses challenge the assumption that abundant precursors automatically give the best identifications. Further validation of the algorithm will require its incorporation by equipment manufacturers into the instrument control programs.