The purpose of discovery proteomics is to gather information about all proteins and protein forms in a biological sample. With only little previous knowlegde of the sample, mass spectrometry-assisted proteomics can identify thousands of proteins and protein forms in a single experiment. Sample fractionation allows for even deeper screening of your samples. Thus, discovery proteomics is typically the first step in any larger proteomics project.

On top of protein identification, mass spectrometry also allows for relative protein quantification. Differential protein analysis enables comparison of protein abundances in differentally treated samples (e.g. cell culture, intact organisms, tissues, plants...)