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

## TL;DR

This paper introduces QuickSearchProt, an algorithm that helps choose optimal search parameters for mass spectrometry data analysis, saving time and effort.

## Contribution

QuickSearchProt is a novel algorithm that automates and accelerates search parameter selection for proteomics data.

## Key findings

- QuickSearchProt processes data sets within minutes using a small representative subset of spectra.
- The algorithm is adaptable and supports X! Tandem and Sage search engines for DDA proteomics data.
- The implementation includes a graphical user interface and is freely available for use.

## Abstract

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.