Although there are a number of variants and side steps that are used for some experiments, optimal analysis of shotgun proteomics experimental data will usually involve most or all of these eight steps: 1) conversion to and processing via open data formats, 2) spectrum identification with a search engine, 3) validation of putative identifications, 4) protein inference, 5) quantification, 6) organization in local data management systems, 7) interpretation of the protein lists, 8) transfer to public data repositories.