Description Usage Format Details Value Source References See Also
Default databases (in
default.LOBdbase), and the .RData files containing
default ranges of structural properties used by
to generate these databases.
Note that the format of these files has changed in LOBSTAHS version 1.1.2 and greater.
Also described is
default.rt.windows, which contains the default
retention time windows (by lipid class) used by
rt.restrict = TRUE.
1 2 3 4 5 6
A list of two
objects, which are the default LOBSTAHS databases for positive and negative
ion mode species, respectively. These were generated using
generateLOBdbase with the default values defined in
A data frame containing empirically-determined adduct ion hierarchy data, by lipid class.
A data frame containing ranges of numbers
of acyl carbon atoms for which in silico data are generated for each
lipid class by
A data frame containing ranges of additional
oxygen atoms to be considered on species of each lipid class when databases
are generated with
A data frame that defines the
elemental compositions of the various adducts, parent lipid "backbones," and
pigments that are used by
A data frame containing the default
retention time data for various lipids and parent lipid classes that are
rt.restrict = TRUE. These
retention time windows are specific to the HPLC-MS method currently used in
the Van Mooy Lab at Woods Hole Oceanographic Institution, where LOBSTAHS was
developed. As described in
doLOBscreen, users outside the Van
Mooy Lab should supply their own retention time data.
Empirical determination of the retention time window data in
default.rt.windows and adduct ion hierarchies in
default.adductHierarchies are described in the references below.
The default ranges for the structural properties given in the other files were
chosen to yield databases that encompass a broad variety of moieites across
lipid types. Microsoft Excel spreadsheet templates are included with the package
in Resources/library/LOBSTAHS/doc for users wishing to modify any of the default
data inputs. Alternatively, the spreadsheet files may be downloaded
from a directory embedded within the package.
These templates can be used to generate .csv files in formats appropriate for
Various list and data.frame objects (as indicated above).
The LOBSTAHS package is presented in:
Collins, J.R., B.R. Edwards, H.F. Fredricks, and B.A.S. Van Mooy. 2016. LOBSTAHS: An adduct-based lipidomics strategy for discovery and identification of oxidative stress biomarkers. Analytical Chemistry 88:7154-7162, doi:10.1021/acs.analchem.6b01260.
Data for lipid classes BLL, PDPT, vGSL, sGSL, hGSL, hapGSL, and hapCER are as described in:
Hunter J. E., M. J. Frada, H. F. Fredricks, A. Vardi, and B. A. S. Van Mooy. 2015. Targeted and untargeted lipidomics of Emiliania huxleyi viral infection and life cycle phases highlights molecular biomarkers of infection, susceptibility, and ploidy. Frontiers in Marine Science 2:81, doi:10.3389/fmars.2015.00081
Fulton, J. M., H. F. Fredricks, K. D. Bidle, A. Vardi, B. J. Kendrick, G. R. DiTullio, and B. A. S. Van Mooy. 2014. Novel molecular determinants of viral susceptibility and resistance in the lipidome of Emiliania huxleyi, Environmental Microbiology 16(4):1137-1149, doi:10.1111/1462-2920.12358.
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