generateLOBdbase {LOBSTAHS} | R Documentation

## Conduct in silico simulation and generate lipid-oxylipin database

### Description

Applies an in silico simulation to generate data by ionization mode (polarity) for a wide range of lipids, oxidized lipids, and oxylipins. User-supplied structural criteria and empirically-determined adduct ion abundance rankings for the major lipid classes are used to create entries for a range of lipid moieties. The database(s) can then be used in `doLOBscreen` to assign compound identities to grouped peakdata.

### Usage

    generateLOBdbase(polarity = c("positive","negative"), gen.csv = FALSE,
                     component.defs = NULL, AIH.defs = NULL, acyl.ranges = NULL,
                     oxy.ranges = NULL)

### Arguments

`polarity` | Ionization mode for which database is to be generated.
`gen.csv` | Should results also be written to a .csv file?
`component.defs` | File path to a .csv file containing elemental composition definitions for the various chemical components needed by `generateLOBdbase`. If nothing is specified, `generateLOBdbase` will use the default composition table (`default.componentCompTable`). The default table includes definitions for the masses of a wide range of adducts, photosynthetic pigments, and structural backbones of some major lipid classes. A Microsoft Excel spreadsheet template included with the package at Resources/library/LOBSTAHS/doc/xlsx/LOBSTAHS_componentCompTable.xlsx can be used to generate a .custom csv file with elemental composition definitions in a format appropriate for `generateLOBdbase`. Alternatively, the spreadsheet may be downloaded from the package GitHub repository. Brief instructions for customization of the table are given in this help document; full instructions, including details on specification of the necessary base fragment, are contained in the package vignette. For each lipid class or compound specified in the component definitions table, the field `DB_gen_compound_type` must contain one of five values: "DB_acyl_iteration," "DB_unique_species," "basic_component," "adduct_pos," or "adduct_neg." The last three compound types are reserved for definition of basic components such as acteonitrile or acetate and for definition of adduct ion types; new entries of these types should only be created in the compound table when a new adduct or basic component must be specified. The first two compound types are used to define the way `generateLOBdbase` creates its databases. There are essentially two ways `generateLOBdbase` creates database entries in LOBSTAHS. For compounds of `DB_gen_compound_type` = "DB_unique_species" (the simpler of the two cases), database entries will be created only for adduct ions of the single compound specified. The latter type should be used for pigments and other lipids that do not have acyl groups, or when the user does not wish to consider any possible variation in acyl properties. In this case, the exact mass of the complete (neutral) molecule should be specified in the component definitions (i.e., component composition) table. Alternatively, for compounds of `DB_gen_compound_type` = "DB_acyl_iteration", `generateLOBdbase` will create database entries for adduct ions of multiple molecular species within the lipid class based on the ranges of acyl properties and oxidation states given for the class in `acyl.ranges` and `oxy.ranges` (see below). In this case, the compound table should be used to define the exact mass of a "base fragment" for the lipid class. Using this "base fragment" as a starting point, `generateLOBdbase` creates multiple entries for molecules in the lipid class by iterative addition of various combinations of fatty acids. In the case of IP-DAG and IP-MAG, the base fragment includes the entire polar headgroup, the glycerol backbone, and both carboxylic oxygen atoms in the fatty acid(s). In the case of TAG, the base fragment is defined as the glycerol backbone plus the carboxylic oxygen atoms on each of the three fatty acids. The base fragments for any new lipid classes for which the user desires evaluation of a range of acyl properties should be similarly defined. Note that regardless of the `DB_gen_compound_type`, an adduct hierarchy must be specified in the adduct ion hierarchy matrix (see below) for each compound or compound class specified in the `Adduct_hierarchy_lookup_class` field of the component definitions table.
`AIH.defs` | File path to a .csv file containing empirical adduct ion hierarchy (AIH) data for various pigments, lipids, and lipid classes. If nothing is specified, `generateLOBdbase` will use the default AIH data (`default.adductHierarchies`). Each compound or compound class for which there is an entry in the AIH definitions table should have at least one corresponding entry in the `Adduct_hierarchy_lookup_class` field of the component definitions table (default, `default.componentCompTable`). A Microsoft Excel spreadsheet template included with the package at Resources/library/LOBSTAHS/doc/xlsx/LOBSTAHS_adductHierarchies.xlsx can be used to generate a .csv file with additional (or alternative) adduct hierarchy data in a format appropriate for `generateLOBdbase`. Alternatively, the spreadsheet may be downloaded from the package GitHub repository.
`acyl.ranges` | File path to a .csv file containing ranges of values for the total number of acyl (i.e., fatty acid) carbon atoms to be considered during the in silico simulation of any lipid classses for which `DB_gen_compound_type` is specified as "DB_acyl_iteration" in the component definitions table, above. These include intact polar diacylglycerols (IP-DAG), triacylglycerols (TAG), polyunsaturated aldehydes (PUAs), and free fatty acids (FFA). If nothing is specified, `generateLOBdbase` will use the default acyl carbon atom range data in (`default.acylRanges`). A Microsoft Excel spreadsheet template included with the package at Resources/library/LOBSTAHS/doc/xlsx/LOBSTAHS_acylRanges.xlsx can be used to generate a .csv file with custom acyl carbon range data in a format appropriate for `generateLOBdbase`. Alternatively, the spreadsheet may be downloaded from the package GitHub repository.
`oxy.ranges` | File path to a .csv file containing ranges of values for the number of additional oxygen atoms to be considered during the in silico simulation of any lipid classses for which `DB_gen_compound_type` is specified as "DB_acyl_iteration" in the component definitions table, above. If nothing is specified, `generateLOBdbase` will use the default oxidation state ranges in (`default.oxyRanges`). A Microsoft Excel spreadsheet template included with the package at Resources/library/LOBSTAHS/doc/xlsx/LOBSTAHS_oxyRanges.xlsx can be used to generate a .csv file with custom oxidation state ranges in a format appropriate for `generateLOBdbase`. Alternatively, the spreadsheet may be downloaded from the package GitHub repository. By default, `generateLOBdbase` considers 0-4 additional oxygen atoms on each chemically possible IP-DAG, TAG, PUA, and FFA.

### Details

Using the default structural property inputs described here, `generateLOBdbase` can produce databases with entries for a wide range of intact polar diacylglycerols (IP-DAG), triacylglycerols (TAG), polyunsaturated aldehydes (PUAs), free fatty acids (FFA), and common photosynthetic pigments. The default databases (as of January 2017) contain data on 18,067 and 15,404 unique compounds that can be identifed in positive and negative ion mode spectra, respectively.

Note that the default databases have been pre-generated (see `default.LOBdbase`) and it is therefore unnecessary to call `generateLOBdbase` with the default parameters.

### Value

A `"LOBdbase-class"` object with the structure:

`frag_ID`:

  Object of class `"integer"`, a unique identifier for this molecular species

`mz`:

  Object of class `"numeric"`, the calculated m/z of this species

`exact_parent_neutral_mass`:

  Object of class `"numeric"`, the calculated (monoisotopic) exact mass of the parent compound of this species

`lipid_class`:

  Object of class `"factor"`, the parent lipid class of this species

`species`:

  Object of class `"character"`, the lipid subclass

`adduct`:

  Object of class `"factor"`, the adduct ion represented by this entry

`adduct_rank`:

  Object of class `"integer"`, the relative abundance ranking of this adduct relative to the other adducts of the same parent compound

`FA_total_no_C`:

  Object of class `"integer"`, total number of acyl (fatty acid) carbon atoms in the parent compound; `NA` if `lipid_class` is not TAG, IP-DAG, PUA, or FFA

`FA_total_no_DB`:

  Object of class `"integer"`, total number of acyl (fatty acid) carbon-carbon double bonds in the parent compound; `NA` if `lipid_class` is not TAG, IP-DAG, PUA, or FFA

`degree_oxidation`:

  Object of class `"integer"`, number of additional oxygen atoms present

`parent_elem_formula`:

  Object of class `"character"`, elemental formula of the parent compound

`parent_compound_name`:

  Object of class `"character"`, name of the parent compound; see the reference for this entry for the naming convention applied to compounds other than pigments

`polarity`:

  Object of class `"factor"`, ionization mode of data in the database

`num_entries`:

  Object of class `"integer"`, number of total entries (adducts) in the database

`num_compounds`:

  Object of class `"integer"`, number of parent compounds represented in the database (should be < `num_entries`)

### Author(s)

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

### 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

`LOBdbase`, `LOBdbase`, `loadLOBdbase`, `doLOBscreen`, `default.LOBdbase`, `default.componentCompTable`, `default.adductHierarchies`, `default.acylRanges`, `default.oxyRanges`

### Examples

    ## generate the default positive ionization mode database

    LOBdbase.pos = generateLOBdbase(polarity = "positive", gen.csv = FALSE,
                                    component.defs = NULL, AIH.defs = NULL,
                                    acyl.ranges = NULL, oxy.ranges = NULL)

[Package LOBSTAHS version 1.14.0 Index]