Measuring Isotope Incorporation in Proteins Produced Using Uniform or Sparse Labeling with 13C and 15N

Sparse labeling is a strategy for isotopic enrichment in proteins grown in mammalian systems, such as glycoproteins. We have developed a customized isotope simulator that can simulate enriched peptide and protein isotope patterns. Using this simulator, we have developed a software to experimentally determine the abundance of ¹³C and ¹⁵N in enriched peptides and proteins using isotope patterns and mass information from conventional mass spectrometers. In addition, we have developed software to determine the percent incorporation of isotope enrichment in sparsely-labeled proteins, in conjunction with isotopic fine structure measurements and MS/MS to assess where incorporation is incomplete or metabolic scrambling has occurred.