Connecting X! Tandem to a Database Management System

Protein identification by mass spectrometry is a valuable method in the field of proteomics and metaproteomics. For protein identification, different protein search engines are used such as X! Tandem, MASCOT, OMSSA, SEQUEST etc. These search engines receive input data in form of files. With the rapid rise of proteomics and metaproteomics, new measurement devices are introduced resulting in increase of research capabilities, consequently producing enormous chunks of data regularly. Admittedly, file-based search engines for protein identification are at their limits and IT methods should be introduced for protein identification to manage huge amount of data efficiently in future. In this paper, we focus on feasibility of Database Management Systems as an alternative to conventional file-based approaches. We implement a connector interface and integrate it into the latest X! Tandem version (2017.02.01) , in order to couple it with a DBMS keeping its business logic intact and study its performance. We compared our work with the core X! Tandem and MetaProteomeAnalyzer tool (which performs protein search and uses a relational database for data storage). We observed there was no information loss in our approach and we were able to successfully implement the DBMS connector interface to X! Tandem.