Back2Basics: mass-to-charge ratio ( m / z ) in proteomics

Large-scale analysis of proteins by shotgun mass spectrometry starts with the measurement of the mass-to-charge ratio ( m / z ) of the peptides. It is important to understand its origin, concept and application to modern day proteomics. The m / z value, defined as the ratio of the peptide mass to the charge it carries, is influenced by the ionization capacity of the peptide. The unit of m / z can be expressed in amu or mmu, with Da (Dalton) commonly used as the de facto unit. The Back2Basics (B2B) article highlights the importance of understanding the spectrum to infer charge state of peptides, and how it is used for the mass determination from the observed m / z . Separation of peptides based on their m / z values is explained, followed by the concept of monoisotopic envelope. Database searching and statistical confidence assessment are also highlighted to provide a well-rounded overview of peptide identification. This B2B article serves as a valuable resource for newcomers as well as seasoned researchers, to facilitate an understanding of the fundamental principles and applications of mass spectrometry in proteomics.