Fig. 6.

Workflow for Strategy1 and Strategy2. Proteins are processed by SpecOMS in order to find the best PSM for each peptide of the database. This is done by computing the shared peaks count (SPC) between every peptide (seen as a theoretical spectrum) of the initial database, compared to all peptides (except itself) from both the target and decoy databases. In Strategy1, the best PSM is chosen according to the raw shared peaks count (or raw SPC). In Strategy2, an extra computation is realized for all candidate PSMs with $\mathrm{\Delta }m\ne 0$, consisting in shifting the peaks according to $\mathrm{\Delta }m$ at all possible locations, and keeping the best induced SPC (or shift SPC)