Fig. 3

Illustration of the Green/Orange/Red classification of PSMs. The first two rows present PSMs with a bait unambiguously deductible from the information given by the PSM. Such PSMs are classified as Green. In the first example, \(\Delta m\) corresponds to the mass of S, which can thus be added in the hit at the given location to retrieve the bait. In the second example, the absolute value of \(\Delta m\) corresponds to the mass of EPPNPE, which can be deleted from the hit to retrieve the bait. In the third row, \(\Delta m\) can correspond to two possible amino acid sequences (VH or HV). Such PSM is thus classified as Orange. In the last three rows, transforming hit into bait is more difficult because there is too much ambiguity, although sequences may be close as in the first red row. In all cases, such PSMs are classified as Red