Mass spectrometry (MS) is the predominant technology for high-throughput analysis to define the protein and post-translational complement of complex biological samples, providing context to biology. As with most high-throughput platforms, data analysis software is crucial for the proper interpretation of the complex data produced by modern instruments. For MS in particular, the proper and complete interpretation of the complex and sometimes multiplexed spectra produced has been an especially challenging problem given the complexity of multitudes of protein sequence possibilities. The primary workhorse of such analysis is the so-called "search engine" that associates mass spectra with proposed peptide interpretations , and the past 25 years have seen a continual development of faster and more sensitive algorithms. However, even with the most recent search engine developments, a substantial amount of post-search-engine processing by additional software is required to yield a final set of identifications of high sensitivity and specificity and accurate abundance information .