Chapter 11: Functional Analysis of Proteins, Including LC-MS and Special Freeware

How do proteins behave? The research area of functional proteomics aims to give answersto this question. A protein has a function in organisms when it is acting as an enzyme (catalyst), when it is regulating as complex (either covalent or non-covalent) and/or when it is transporting compounds via noncovalent complexes. Many analytical techniques can be applied for the characterization of protein function. This chapter describes an example LC-MS strategy analysing biofunctionality such as stable non-covalent enzyme–inhibitor complexes and the application of a software tool specially developed for such experimental strategies. Practical information is given about the experimental setup and the software tool. In addition, tips and tricks aim to avoid problems and pitfalls.