build.homol: Build molecular formulae for a homologue series

In schymane/RChemMass: Various Cheminformatic, Curation and Mass Spectrometry Functions

Description

Given a starting formula and a "building block", this builds a series for formulas from n_start to n_max, adding a retention time for direct use in suspect screening. Naming is built on series_name and n. Formula manipulations are performed with enviPat and RMassBank. Can be used if generic structures are not available for buildSmiles.

Usage

build.homol(start_formula, building_block, series_name, n_start, n_max, rt=15)

Arguments

start_formula	Molecular formula to start building the series. Standardised with checkform, along with building_block.
building_block	Formula of the "building block" to add n times to start_formula.
series_name	Codename for the series. Short names are recommended for downstream use.
n_start	Starting number for member naming only. Formula building goes from n=1 ( start_formula) to n=(n_max-n_start).
n_max	Maximum number to calculate.
rt	Default 15 (minutes); can be adjusted for different systems and anticipated series behaviour as desired. For first round screening, RT in the middle of the elution is recommended, such that a symmetrical window over the whole program can be used.

Value

Returns a n_max-n_start by 4 array containing member names, formulas, RTs and neutral monoisotopic mass.

Author(s)

Emma Schymanski <[e-mail]>

See Also

buildSmiles, check_chemform, mergeform, enviPat, findMz.formula.

Examples

las <- build.homol("C16H26O3S","CH2","LAS",10,14)
spacs <- build.homol("C9H10O5S","CH2","SPAC",3,15)
spadcs <- build.homol("C9H8O7S","CH2","SPADC",1,15)
c12aes <- build.homol("C14H30O5S","C2H4O","C12AES",1,10)
c13aes <- build.homol("C15H32O5S","C2H4O","C13AES",1,6)
npeos <- build.homol("C17H28O5S","C2H4O","NPEO_SO4_",1,8)

schymane/RChemMass documentation built on Jan. 25, 2021, 5:45 a.m.