Memory-Efficient Searching of Gas-Chromatography Mass Spectra Accelerated by Prescreening

Abstract

The number of metabolomics studies and spectral libraries for compound annotation (i.e., assigning possible compound identities to a fragmentation spectrum) has been growing steadily in recent years. Accompanying this growth is the number of mass spectra available for searching through those libraries. As the size of spectral libraries grows, accurate and fast compound annotation becomes more challenging. We herein report a prescreening algorithm that was developed to address the speed of spectral search under the constraint of low memory requirements. This prescreening has been incorporated into the Automated Data Analysis Pipeline Spectral Knowledgebase (ADAP-KDB) and can be applied to compound annotation by searching other spectral libraries as well. Performance of the prescreening algorithm was evaluated for different sets of parameters and compared to the original ADAP-KDB spectral search and the MSSearch software. The comparison has demonstrated that the new algorithm is about four-times faster than the original when searching for low-resolution mass spectra, and about as fast as the original when searching for high-resolution mass spectra. However, the new algorithm is still slower than MSSearch due to the relational database design of the former. The new search workflow can be tried out at the ADAP-KDB web portal.