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. Author manuscript; available in PMC: 2022 Aug 6.
Published in final edited form as: J Proteome Res. 2021 Jul 8;20(8):4153–4164. doi: 10.1021/acs.jproteome.1c00483

Figure 1: Graphical overview of methods.

Figure 1:

“Keep relevant” means that any PSM that involves a relevant peptide is kept while every other PSM is removed. “Keep irrelevant” means any PSM that involves an irrelevant peptide is kept while every other PSM is removed. Neighbor peptides are defined and explicitly considered separate from irrelevant peptides only in “subset-neighbor search” (SNS). The difference between C and E is the input into the “score + keep relevant” box. The input to E are neighbor and relevant peptides. The input to C are irrelevant peptides, which includes neighbor peptides, and relevant peptides.