Query tabular loads a tabular database and creates a sqlite database and tabular file. To learn more about SQL Queries - please look at this documentation.
The help section on the Query Tabular tool provides simple examples of both filtering the input tabular datasets, as well as examples of SQL queries. Query Tabular also incorporates regex functions that can be used queries. The PSM report datasets in these tutorials have fields that are lists of protein IDs.
Query Tabular help shows how to normalize those protein list fields so that we can perform operations by protein ID. See section: Normalizing by Line Filtering into 2 Tables in the tool help (below the tool in Galaxy).