text: A major challenge for lipidomics, in particular for MS-based approaches, lies in the computational and bioinformatic demands of handling the large amount of data that arise at various stages along the chain of information acquisition and processing.
   Chromatographic and MS data collection requires substantial efforts in spectral alignment and statistical evaluation of fluctuations in signal intensities. Such variations have a multitude of origins, including biological variations, sample handling and analytical accuracy. As a consequence several replicates are normally required for reliable determination of lipid levels in complex mixtures. Within the last few years, a number of software packages have been developed by various companies and research groups to analyze data generated by MS profiling of metabolites, including lipids. The data processing for differential profiling usually proceed through several stages, including input file manipulation, spectral filtering, peak detection, chromatographic alignment, normalization, visualization, and data export. An example of metabolic profiling software is the freely-available Java-based Mzmine application. Another is Metabolon, Inc’s commercial applications for metabolomic analysis using proprietary software. Recently [http://prime.psc.riken.jp/compms/msdial/main.html MS-DIAL 4] software was integrated with a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information for 117 lipid subclasses and 8,051 lipids. Some software packages such as Markerview include multivariate statistical analysis (for example, principal component analysis) and these will be helpful for the identification of correlations in lipid metabolites that are associated with a physiological phenotype, in particular for the development of lipid-based biomarkers. Another objective of the information technology side of lipidomics involves the construction of metabolic maps from data on lipid structures and lipid-related protein and genes. Some of these lipid pathways are extremely complex, for example the mammalian glycosphingolipid pathway. The establishment of searchable and interactive databases of lipids and lipid-related genes/proteins is also an extremely important resource as a reference for the lipidomics community. Integration of these databases with MS and other experimental data, as well as with metabolic networks offers an opportunity to devise therapeutic strategies to prevent or reverse these pathological states involving dysfunction of lipid-related processes.