For some years now, scientists have been spending a lot of effort in developing methods to analyse and compare complex protein samples. One of the goals of such global analyses of what is known as proteomes is to discover specific protein markers–or fingerprints of protein markers−from various types of affected biological samples. Considering the battery of technologies currently available, mass spectrometry (MS) constitutes an essential tool in proteomics. We describe here the type of MS instrumentation that is currently dedicated to proteomics research. We also describe the major experimental workflows that are typically used in proteomics today, with a focus on those incorporating MS as a major analysis tool.