Accurate mass searching of individual lipid species candidates from high-resolution mass spectra for shotgun lipidomics.

RATIONALE: With the increased mass accuracy and resolution in commercialized mass spectrometers, new developments on shotgun lipidomics could be expected with increased speed, dynamic range, and coverage over lipid species and classes. However, we found that the major issue by using high mass accuracy/resolution instruments to search lipid species is the partial overlap between the two-(13) C-atom-containing isotopologue of a species M (i.e., M+2 isotopologue) and the ion of a species with one less double bond than M (assigned here as L). This partial overlap alone could cause a mass shift of the species L to the lower mass end up to 12 ppm around m/z 750 as well as significant peak broadening.
METHODS: We developed an approach for accurate mass searching by exploring one of the major features of shotgun lipidomics data that lipid species of a class are present in ion clusters where neighboring masses from different species differ by one or a few double bonds. In the approach, a mass-searching window of 18 ppm (from -15 to 3 ppm) was first searched for an entire group of species of a lipid class. Then accurate mass searching of the plus one (13)C isotopologue of individual species was used to eliminate the potential false positive.
RESULTS: The approach was extensively validated through comparing with the species determined by the multi-dimensional MS-based shotgun lipidomics platform. The newly developed strategy of accurate mass searching enables the overlapped L species to be identified and the corresponding peak intensities to be acquired.
CONCLUSIONS: We believe that this novel approach could substantially broaden the applications of high mass accurate/resolution mass spectrometry for shotgun lipidomics.