title: Software tools for analysis of mass spectrometric lipidome data.
abstract: New software tools for quantitative analysis of mass spectrometric lipidome data have been developed. The LIMSA tool finds and integrates peaks in a mass spectrum, matches the peaks with a user-supplied list of expected lipids, corrects for overlap in their isotopic patterns, and quantifies the identified lipid species according to internal standards. Three different algorithms for isotopic correction (deconvolution) were implemented and compared. LIMSA has a convenient user interface and can be applied on any type of MS spectrum. Typically, analysis of one spectrum takes only a few seconds. The SECD tool, designed for analysis of LC-MS data sets, provides an intuitive and informative display of MS chromatograms as two-dimensional "maps" for visual inspection of the data and allows the user to extract mass spectra, to be further analyzed with LIMSA, from arbitrary regions of these maps. More reliable analysis of complex lipidome data with improved signal-to-noise ratio is obtained when compared to standard time-range averaged spectra. The functionality of these tools is demonstrated by analysis of standard mixtures as well as complex biological samples. The tools described here make accurate, high-throughput analysis of extensive sample sets feasible and are made available to the scientific community free of charge.
authors.affiliation: Institute of Biomedicine, Department of Biochemistry, University of Helsinki, Haartmaninkatu 8, PL 8, 00014 Helsinki, Finland.
authors.forename: Perttu
authors.initials: P
authors.lastname: Haimi
authors.forename: Andreas
authors.initials: A
authors.lastname: Uphoff
authors.forename: Martin
authors.initials: M
authors.lastname: Hermansson
authors.forename: Pentti
authors.initials: P
authors.lastname: Somerharju
mesh_terms: D019295:Computational Biology; D001330:Electronic Data Processing; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods*; D008055:Lipids / Q000032:analysis*; D012984:Software
chemical_list: D008055:Lipids