Screenshot of the MassShiftFinder main window. The data are taken from an experiment on guanidinated enolase (see additional file 2: ExperimentalExamples.pdf). The mass shift boundaries are set to restrict the detected mass shift mainly to guanidinations (mass shift of 42 Da). The highlighted row (14) indicates an "X-Z" mass shift (see Figure 1). Rows 11–13 show a mass shift occurring in the Y-area, with one tryptic peptide (1316.7) paring up with three chymotryptic peptides. The right-most column (UniMod hits) for most of the rows indicates that there are three modifications (acetylation, tri-methylation and guanidination) that are consistent with a mass shift of 42 for the indicated peptides. Row 16 has 0 UniMod hits because the calculated mass shift is more than 0.1 Da from the three mentioned modifications; furthermore, this mass shift cannot be due to guanidinated K as only one of the peptides contains a K.