This course aims to teach the fundamentals of biological mass spectrometry with particular focus on applications to proteomics and analysis of protein modifications. The course will begin with an introduction to the general aspects of mass spectrometry-based peptide sequencing and protein identification, along with recent technological developments in the context of advancing quantitative shotgun proteomic analysis. Current perspectives in global versus directed analysis, speed versus depth in proteomic coverage, will be discussed. This will then be followed by introducing the practical aspects of MS analysis of select protein modifications, at both the levels of single targeted protein of interest and the proteomic scale. Topics include phosphoproteomics; lysine modifications such as acetylation, methylation, ubiquitination, and SUMOylation; cysteine modifications such as oxidation, glutathionylation and S-nitrosylation; and glycosylation. The last further accompanied by an overview of MS-based glycomics and glycoproteomics.