Abstract

In mass spectrometry based proteomics experiments, peptides are assigned to experimentally acquired tandem mass spectra (MS2) by a method called peptide-spectral matching. Peptide spectral matching is commonly achieved by using search algorithms to match the acquired MS2 spectra to theoretical spectra. The theoretical spectra are generated from an in silico digestion and fragmentation of proteins in the FASTA database. Ideally, the protein FASTA databases will contain all proteins of the organism under investigation.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• How to download protein FASTA databases of a certain organism?
• How to download a contaminant database?
• How to create a decoy database?
• How to combine databases?

Learning Objectives

• Creation of a protein FASTA database ready for use with database search algorithms.