Annotation for Structure of Lipid Species

Although many systematic indices (e.g.. Lipid MAPS, Chemical Entries of Biological Interest (ChEBI), lUPAC International Chemical Identifiers (InChl), simplified molecular-input line entry system (SMILES)) were developed to list the chemical compounds, these indices (identifiers) can only be meaningful if the compound is totally identified. However, in practice, lipidomics analysis in many cases can only provide partial identification of lipid molecular structures at the current development of technology. Moreover, different lipidomics approaches provide different levels of stmctural identification of lipid species. Therefore, how to clearly express and report the information about the levels of identification for the structures of lipid species (which can be derived fi om MS analysis) is not only helpful for the readers but also important for bioinformatics and data communication. To this end, the analysis by shotgun lipidomics could be used as a typical example to explain these levels. Similar phenomena also exist in the analysis of lipid species employing LC-MS-based approaches. 

In the high mass accuracy/resolution mass spectrometry-based shotgun lipidomics approach, the overlaps between SM and M-f1 C isotopologue of PC species, and between PC subclasses can be resolved [35]. Moreover, the linkages of alkyl vs. alkenyl at the sn-1 position of glycerol and the fatty acyl chains of diacyl species are also identified by product-ion analysis [35,36]. Clearly, this approach provides much more structural information than that of the tandem MS approach as aforementioned. 

In the MDMS-SL approach, in addition to identification of the overlaps and the identities of fatty acyl chains, the location of those FA chains (i.e., regioisomers) in diacyl PC species can also be accessed [3,37]. Furthermore, even the location of double bonds in the fatty acyl chains can be identified with efforts [38]. Therefore, these types of additional structural information should be reflected from the data report. 

To reflect these different levels of structural information, a system of shorthand notation for lipid structures derived from MS analysis was proposed [39] and becomes widely accepted. For example, for analysis of PC species, it was proposed to notate with PC(nominal mass) or PC(m n) to represent a detected species by the tandem MS approach (where m and n are the total number of carbon atoms and double bonds of aliphatic chains in the species, respectively) with PC(mi i i2 2) or PC(o-mi ni m2 2) to reflect the identification of individual fatty acyl chains and the ether bond by the high mass resolution mass spectrometry-based shotgun lipidomics and with VCim1.n1lm2.n2) or VCio-m1.n1lm2.n2) to denote the total identification of PC species by MDMS-SL. Similarly, MRM-based methods after 

LC-MS should be only denoted with PC(m n) and data-dependent acquisition methods after LC-MS could be expressed the latter cases as described earlier. 

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