Automatic Selection of Search Parameter Values for Mass Spectrometry-Based Search Engines

A crucial step in processing mass spectrometry-based proteomics data is identifying and quantifying the proteins in the sample. While the existing search engines can easily match tandem mass spectra to peptide sequences, selecting the most appropriate search parameters can often be challenging and time-consuming due to the diversity of the data sets and the long list of available parameter values to choose from. This study introduces QuickSearchProt─an algorithm aimed at assisting in the selection of search parameter values across search engines, considering not only the data set specifications but also the properties of the search algorithms. By relying on a small representative subset of the spectra, the algorithm can process most data sets within minutes, largely independent of the size of the original data set. The current implementation supports two common search engines, X! Tandem and Sage, and is designed to process data-dependent acquisition (DDA) proteomics data sets but due to its adaptability and scalability can easily be extended to additional search engines. QuickSearchProt, including a graphical user interface, the complete source code, and additional details are freely available at http://www.github.com/barsnes-group/QuickSearchProt.