Protein Identification by Database Searching of Mass Spectrometry Data in the Teaching of Proteomics

Mass spectrometry is essential for large-scale protein identification in proteomics. By database searching of mass spectrometry data, it is possible to identify proteins without the need to interpret MS/MS spectra (de novo sequencing), which is time-consuming and not feasible as a systematic tool in proteomic analysis. Many authors have reported initiatives to teach protein mass spectrometry to undergraduate students, but database searching is usually not emphasized. Here, we propose a class about database searching of mass spectrometry data for protein identification in order to complement a theoretical proteomics course. It includes a presentation about the theory of database searching and a practical, computer-based activity in which students can learn how to perform analysis of mass spectrometry data for proteomics purposes. Our class model fills a widespread gap in the teaching of proteomics and improves students' understanding of protein identification by mass spectrometry.