Mass spectrometry based proteomics studies typically aim at measuring and comparing changes in biological samples. This however strongly relies on our ability to interpret the massive amounts of data produced by modern mass spectrometers. Therefore, methods and tools have been developed to tackle four major topics:

• Identification
• Functional Analysis
• Data Sharing
• Quantification

This tutorial aims at providing the basis for any user to go through the following workflow: (1) identify peptides, proteins, and their modifications, (2) annotate the data with existing biological knowledge, and (3) share the data using online repositories. Finally, the different techniques for quantifying peptides and proteins will be introduced.