In a time frame of a few decades, protein identification went from laborious single protein identification to automated identification of entire proteomes. This shift was enabled by the emergence of peptide-centric, gel-free analyses, in particular the so-called shotgun approaches, which not only rely on extensive experiments, but also on cutting-edge data processing methods. The present review therefore provides an overview of a shotgun proteomics identification workflow, listing the state-of-the-art methods involved and software that implement these. The authors focus on freely available tools where possible. Finally, data analysis in the context of emerging across-omics studies will also be discussed briefly, where proteomics goes beyond merely delivering a list of protein accession numbers.