Screenshots of the ALEX target list generator and ALEX extractor.

(A) The ALEX target list generator allows users to select lipid classes and species to be identified using criteria such as lipid class, adduction, C index, db index and OH index. Individual lipid species including internal standards can also be selected. The ALEX target list generator output is a .txt file with a shortlist of selected lipid species, respective m/z values and accessory lipid features. The ALEX target list generator also supports inclusion of isotope information that can be used for deisotoping and isotope correction [20] by applying algorithms within the auxiliary workflow. (B) The ALEX extractor identifies lipid species, exports intensity data and incorporates accessory lipid features. As input the ALEX extractor requires the location of spectral peak lists generated by the ALEX converter, a target list compiled by the ALEX target list generator and a location to deposit output files. The ALEX extractor features options to specify an m/z tolerance window for lipid identification, to apply a constant m/z offset to correct lipid searches for a constant FT MS calibration offset or to apply a lock mass adjustment routine that automatically corrects lipid searches for drifts in FT MS calibration. The automated lock mass adjustment routine requires specification of well-characterized and ubiquitous lock mass ions in order to estimate the FT MS calibration offset.