In another application, mass spectrometry helps to identify post-translational products over expressed in E-Coli or other organisms. For example, recombinant P. furiosus rubredoxins are expressed in multiple forms, as the wild-type (without an N-terminal methionine), a form containing an N-terminal methionine, and a form containing formyl-N-terminal methionine. Samples of these forms are collected during the chromatographic steps of the protein purification procedure using anion exchange and hydroxyapatit and then submitted for LC-MS or MALDI, and the resulting molecular weights compared with theoretical molecular weights. The mass spectrometry determined molecular weights are typically within 1 atomic mass unit of the theoretical molecular weight and unambiguously identify the three forms of rubredoxin.

LC-MS is also a valuable means of assessing protein purity. The rubredoxins mentioned differ only slightly in molecular weights (+130 and +159 u for the N-terminal Met and formyl-N-terminal Met forms, respectively) and these factors make protein purification difficult. When a rubredoxin is purified, its purity is checked by LC-MS which shows the relative abundance of the forms of rubredoxin present. For example, LC-MS of a rubredoxin of the wild-type sequence (without an N-terminal methionine) that has been extensively purified may reveal 5% of the N-terminal Met form present in the sample, or in a better purification, it may reveal no other forms of rubredoxin present. In the latter case, the rubredoxin would be considered purified and ready for its intended purpose.