LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.
|Author||James Collins [aut, cre], Helen Fredricks [aut], Bethanie Edwards [aut], Benjamin Van Mooy [aut]|
|Date of publication||None|
|Maintainer||James Collins <firstname.lastname@example.org>|
|License||GPL (>= 3) + file LICENSE|
doLOBscreen: Screen, annotate, and identify compounds in an xsAnnotate...
extractLOBdbasedata: Extract compound data from a LOBdbase
generateLOBdbase: Conduct _in silico_ simulation and generate lipid-oxylipin...
getLOBpeaklist: Export screened LOBSTAHS peaklist with compound assignments
loadLOBdbase: Import and reconstruct LOBdbase from a text file
LOBdbase: LOBdbase constructor for manual creation or reconstruction of...
LOBdbase-class: Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
LOBdefaults: LOBSTAHS default databases and database generation parameters
LOBSet: LOBSet constructor for manual creation or reconstruction of a...
LOBSet-class: Class LOBSet: Peak data with annotations, isomers, and...