LOBdefaults: LOBSTAHS default databases and database generation parameters

In LOBSTAHS: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

Description

Default databases (in default.LOBdbase), and the .RData files containing default ranges of structural properties used by generateLOBdbase 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 doLOBscreen when rt.restrict = TRUE.

Usage

data(default.LOBdbase)
data(default.adductHierarchies)
data(default.acylRanges)
data(default.oxyRanges)
data(default.componentCompTable)
data(default.rt.windows)

Format

default.LOBdbase

A list of two "LOBdbase" 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 default.adductHierarchies, default.acylRanges, default.oxyRanges, and default.componentCompTable.

default.adductHierarchies

A data frame containing empirically-determined adduct ion hierarchy data, by lipid class.

default.acylRanges

A data frame containing ranges of numbers of acyl carbon atoms for which in silico data are generated for each lipid class by generateLOBdbase.

default.oxyRanges

A data frame containing ranges of additional oxygen atoms to be considered on species of each lipid class when databases are generated with generateLOBdbase.

default.componentCompTable

A data frame that defines the elemental compositions of the various adducts, parent lipid "backbones," and pigments that are used by generateLOBdbase.

default.rt.windows

A data frame containing the default retention time data for various lipids and parent lipid classes that are used by doLOBscreen when 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.

Details

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 generateLOBdbase and doLOBscreen.

Value

Various list and data.frame objects (as indicated above).

Source

http://github.com/vanmooylipidomics/LOBSTAHS/

References

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.

See Also

doLOBscreen, generateLOBdbase, LOBdbase LOBdbase

LOBSTAHS documentation built on Nov. 8, 2020, 6:47 p.m.