Mass spectrometry and computational proteomics

Mass Spectrometry is the tool of choice for proteomics, with applications to peptide sequencing, protein structure prediction, protein–protein interactions, and many others. Continued improvements in instrumentation and computational technologies will only help accelerate this trend. A short overview of algorithms for interpreting mass spectrometry (MS) data is provided. This overview is not intended as an introduction to the technology itself or to proteomics. Instead, an abstract overview of MS data is presented in order to describe key algorithmic ideas required for its interpretation. Three proteomic applications are considered: protein identification, protein interactions, and differential analysis of protein expression.

Keywords: de novo sequencing; dynamic programming; electrospray; MALDI; mass spectrometry; tandem mass spectrometry; proteomics