A recent paper published by Chu et al. (2015) gives an overview of work presented at the Mass Spectrometry and Proteomics Workshop held at the University of Hong Kong in December 2014.1 The paper contains proposals for improving the nomenclature used to describe peptide ions resulting from mass spectrometry analysis. The authors intend that the new system should increase clarity and decrease ambiguity for researchers when denoting ion fragments encountered during mass spectrometry evaluation.
Mass spectrometry–based proteomic analysis presents multiple techniques for fragmenting protein digests from a number of samples. Each different fragmentation tool creates a diverse mixture of ion types, which need adequate and unambiguous description for future research, review and collaboration. Not only does a system have to describe the type of fragment, but it must also correctly ascribe charge states, hydrogen losses and gains, and presence of radicals to the correct position within the particle created. From the information given, researchers should be able to deduce the peptide fragments and thereby identify the proteins under investigation.
Current systems for denoting peptide ions describe fragments according to type, denote whether they retain charge on the N-terminus or the C-terminus, give positional information within the chain, show charge state, and indicate hydrogen gain or loss. Naming systems that are more complicated can cope with the radical cationic products produced during ECD (electron capture dissociation) and ETD (electron transfer dissociation), and with complex products from anionic peptides. Many systems have developed by expanding upon and simplifying existing methods as mass spectrometry techniques advance, and according to researcher needs.
Although systems already exist to describe peptide ion fragments, Chu et al. propose that developing and adopting a new nomenclature could be more inclusive and less open to misinterpretation. Their proposal encompasses the three recommendations made by the team:
- All variables must be shown explicitly
- All lettering should be in regular font and lowercase to avoid confusion with existing systems already in use
- Square brackets should denote hydrogen ion involvement
The nomenclature proposed uses a linear notation for sequences, adding square brackets to deal with longer peptides.
According to the team, this proposal should clarify radical ions that are rich in hydrogen additions and show stoichiometry in better detail. Moreover, Chu et al. maintain that the proposed nomenclature is an improvement for detailing radical peptide fragmentation.
1. Chu, I.K., et al. (2015) “Proposed nomenclature for peptide ion fragmentation,” International Journal of Mass Spectrometry, 390 (pp. 24–7).