doLOBscreen: Screen, annotate, and identify compounds in an xsAnnotate...
In LOBSTAHS: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

Description Usage Arguments Details Value Author(s) References See Also Examples

Primary function of the LOBSTAHS package. Screen, annotate, and assign compound identities to peak groups in a CAMERA xsAnnotate object containing HPLC-ESI-MS lipid data. Identify and annotate possible isomers and isobars.

1
2
3

doLOBscreen(xsA, polarity = NULL, database = NULL, remove.iso = TRUE,
            rt.restrict =  TRUE, rt.windows = NULL, exclude.oddFA = TRUE,
            match.ppm = NULL, retain.unidentified = TRUE)

`xsA`	A CAMERA `xsAnnotate-class` object with identified pseudospectra. Must contain isotope data from `findIsotopes` if user elects `remove.iso = TRUE`).
`polarity`	Specify polarity mode of data in `xsA`: "positive" or "negative." `doLOBscreen` will attempt to detect the polarity mode if nothing is given.
`database`	Specify the `LOBdbase` from which compound identities and adduct ion hierarchy data are to be applied. If nothing is specified, `doLOBscreen` will use the LOBSTAHS default database (`default.LOBdbase`) for the appropriate ionization mode. The database generation function `generateLOBdbase` can be used to create a LOBdbase from structural property ranges specified by the user in a series of input tables. `loadLOBdbase` can be used to import and reconstruct a `"LOBdbase"` object from a previously generated database that was saved as a .csv file.
`remove.iso`	Should secondary isotope peaks be removed? (If `TRUE`, `xsA` must contain isotope data obtained using `findIsotopes`.)
`rt.restrict`	Should lipid class retention time screening criteria be applied to putative compound assignments?
`rt.windows`	File path to a .csv file containing retention time "window" data to be used for screening by lipid class, if `rt.restrict = TRUE`. If nothing is specified, `doLOBscreen` will use the package default windows (`default.rt.windows`), which are specific to the HPLC-MS method currently used in the Van Mooy Lab at Woods Hole Oceanographic Institution. Because the user is advised to provide retention time data specific to his/her HPLC-MS method, failure to specify a value for `rt.windows` will result in a warning. A Microsoft Excel spreadsheet template included with the package at Resources/library/LOBSTAHS/doc/xlsx/LOBSTAHS_rt.windows.xlsx can be used to generate a .csv file of retention time data in a format appropriate for `rt.windows`. Alternatively, the spreadsheet file may be downloaded from the package GitHub repository.
`exclude.oddFA`	Should compound assignments with an odd total number of acyl carbon atoms be excluded? (Applies only to assignments where the parent lipid class is TAG, IP-DAG, PUA, or FFA.) Useful if data are (or are believed to be) of exclusively eukaryotic origin.
`match.ppm`	m/z tolerance (in ppm) used for matching observed data against the calculated m/z's in the database
`retain.unidentified`	Should data for unidentified or discarded features be retained and appended to user's results? Useful if untargeted follow-on data analysis is anticipated, or when user wants to retain data for all features present in the original dataset, not just those for which a LOBSTAHS identity was found.

doLOBscreen draws compound identities from a LOBdbase database. The function applies various retention time and adduct ion hierarchy screening criteria to winnow the list of putative compound assignments. It returns a table of annotated peak data with compound assignments and various annotation codes to assist the user in interpretation and follow-on data analysis.

A "LOBSet-class" object.

James Collins, james.r.collins@aya.yale.edu

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.

LOBSet, LOBdbase, loadLOBdbase, getLOBpeaklist, generateLOBdbase, default.LOBdbase, default.rt.windows, xcmsSet, xsAnnotate, findIsotopes

## screen & annotate xsAnnotate object from the PtH2O2lipids dataset using all
## screening options, while retaining unidentified/discarded features
library(PtH2O2lipids)


myPtH202LOBSet = doLOBscreen(ptH2O2lipids$xsAnnotate, polarity = "positive",
                             database = NULL, remove.iso = TRUE,
                             rt.restrict =  TRUE, rt.windows = NULL,
                             exclude.oddFA = TRUE, match.ppm = 2.5,
                             retain.unidentified = TRUE)

## show some diagnostics
LOBscreen_diagnostics(myPtH202LOBSet) # screening diagnostics
LOBisoID_diagnostics(myPtH202LOBSet) # isomer identification data