Procedures for mass spectrometric proteome analysis

Abstract

Any kind of protein or protein mixture can be analysed by mass spectrometry (MS) to identify proteins. The proteins are cleaved with an endopeptidase, like trypsin, and the peptides are analysed by MS. The data are used for database screening. The classical approach uses 2D gel-electrophoresis to separate protein mixtures. Individual spots can be cut out and analysed. Other approaches omit the 2D gels and use chromatographic procedures to separate the peptides before the mass spectrometric analysis. Here, we describe the procedures for the analysis of spots from 2D gels (or bands from 1D gels) with an LCQ mass spectrometer (Finnigan, San Jose, USA) using nanospray sample application. Work for the analysis of protein mixtures and use of 2D-chromatography is in progress.