A support for the identification of non-tryptic peptides based on low resolution tandem and sequential mass spectrometry data: The INSPIRE software

A simple software, to be used as an aid in the identification of non-tryptic peptides based on low resolution (3D-ion trap) tandem (MS/MS) and sequential (MS3) mass spectrometry data, is presented. The program, named INSPIRE (Identification of Non-tryptic peptide Sequences based on Product Ions m/z ratios and RElative abundances), provides alternative rankings for the several candidate sequences usually arising from protein database searches when non-tryptic peptides are involved and only low resolution MS/MS data are available. The rankings, based on parameters related to m/z ratios and relative abundances of experimental product ions matching with predicted ones, can be exploited to reduce the number of candidates to be included in subsequent data processing based on MS3 measurements. The latter usually represents a mandatory step towards a reliable peptide identification when high resolution MS/MS data are not accessible. Sets of peptide sequences arising from MS/MS-based database searches for 63 previously identified non-tryptic peptides (all generated from milk proteins) were exploited to check the INSPIRE performance. It was found that, if retrieved among candidates after the database search, the correct sequence was always ranked among the first 10 ones when parameters calculated by INSPIRE were adopted for discrimination purposes. Under the same conditions the ranks provided by popular database search programs were significantly worse in a remarkable number of cases.