Peptide identification from MS/MS spectra is a key step in bottom-up mass spectrometrybased proteomics. Since the mid-1990's, a plethora of specialized software, called proteomics search engines, have been developed to automate peptide identification. These search engines generally take two inputs: a spectrum file originating from the mass spectrometer, potentially preprocessed, and a FASTA protein sequence file. Then the output in its simplest form is a list of identified peptides with peptide-spectrum match (PSM) information. This PSM list is then usually passed on to other bioinformatics tools for further downstream analysis step(s), such as identification rescoring, protein inference, or protein quantification.