Analysis of the proteome of cell populations by sub-compartment. Proteomics is particularly informative when applied to individual cellular compartments, such as the cell surface, secretome, the nucleus or other organelles, for which isolation and analysis procedures are required. Moreover, aside from the identification of constituent proteins, there is a need to assess post-translational modifications (PTMs) of proteins, including major modifications such as phosphorylation and glycosylation, in addition to cleavage and proteolysis. Cell surface proteins (for example, receptors and antigens) may be captured through the use of lipid impermeable biotin followed by capture of surface proteins using monomeric avidin and subsequent mass spectrometry (MS) analysis. Proteins in cell culture media may be fractionated as intact proteins using chromatography followed by digestion of individual fractions and MS analysis. Alternatively, particulate material (for example, exosomes) may be first isolated from media, followed by their MS analysis separately from the soluble fraction in the media.