Implementation of data-dependent isotopologue fragmentation in 13C-based metabolic flux analysis

A novel analytical approach based on liquid chromatography coupled to quadrupole time of flight mass spectrometry, employing data-dependent triggering for analysis of isotopologue and tandem mass isotopomer fractions of metabolites of the primary carbon metabolism was developed. The implemented QTOFMS method employs automated MS/MS triggering of higher abundant, biologically relevant isotopologues for generating positional information of the respective metabolite. Using this advanced isotopologue selective fragmentation approach enables the generation of significant tandem mass isotopomer data within a short cycle time without compromising sensitivity. Due to a lack of suitable reference material certified for isotopologue ratios, a Pichia pastoris cell extract with a defined 13C distribution as well as a cell extract from a 13C-based metabolic flux experiment were employed for proof of concept. Moreover, a method inter-comparison with an already established GC-CI-(Q)TOFMS approach was conducted. Both methods showed good agreement on isotopologue and tandem mass isotopomer distributions for the two different cell extracts. Graphical abstract Schematic overview of data-dependent isotopologue fragmentation for acquisition of isotopologue and tandem mass isotopomer fractions.