Introduction to Proteomics

Mass spectrometry (MS) has recently become one of the most informative methods for studying proteins. Albiet, MS cannot compete with the detailed structural information obtained by methods such as nuclear magnetic resonance and X-ray crystallography. However, MS is much easier to automate and use as a large-scale technique. Large-scale proteomic methods are valuable for studying the dynamics of the proteins and their posttranslational modification in living cells. Despite the great potential of mass spectrometers, many laboratories are struggling with data analysis and data storage. The complexity of the data analysis stems from the large number of experiments that can be performed by various mass spectrometers. In addition, many mass spectrometers have their own data formats. Performing data analysis on MS data, therefore, requires a rather extensive setup of algorithms and data parsers. In recent years it has become evident that the proteomics society needs standard formats for storing and exchanging data. This has triggered a new problem, which is the invention of several different standard formats. In this chapter, an overview of the most common proteomics experiments with MS, together with an overview of data formats, is presented.