. 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

Table 1: Summary of methods.

We represent irrelevant peptides with an ‘I’, neighbor peptides with an ‘N’, and relevant peptides with an ‘R’. If a database consists of multiple groups of peptides, then a ‘+’ is used. Therefore, a database consisting of both relevant and neighbor peptides would be represented as ‘R+N’. Group-FDR is with respect to R for the “Database to Search” step.

	search-then-select	subset-search	all-sub	group-FDR	SNS
Consider neighbor peptides?					✓
Database to search	R+I+N	R	R+I+N	R+I+N	R+N
Apply group-FDR?			variation	✓	✓