gcxgclab (version 1.0.1)

non_targeted: Compares MS to atomic mass data

Description

non_targeted compares the MS data from a peak to atomic mass data.

Usage

non_targeted(masslist, ms, THR = 0.1, ...)

Value

A list object, a list of vectors containing strings of the matching compounds.

Arguments

masslist

a list object, a list of atomic weights, ideally the output of mass_list().

ms

a data.frame object, a data frame of the mass values and the percent intensity values, ideally the output of find_ms().

THR

a double object. The threshold of intensity of which to include peaks for mass comparison. Default is 0.1.

...

a vector object. Any further optional inputs which indicate additional elements to consider in the compound, or restrictions on the number of a certain element in the compound. Should be in the form c('X', a, b) where X = element symbol, a = minimum number of atoms, b = maximum number of atoms. a and b are optional. If no minimum, use a=0, if no maximum, do not include b.

Details

This function takes the MS data from an intensity peak in a sample and compares it to combinations of atomic masses. Then it approximates the makeup of the compound, giving the best matches to the MS data. Note that the default matches will contain only H, N, C, O, F, Cl, Br, I, and Si. The user can input optional parameters to indicate additional elements to be considered or restrictions on the number of any specific element in the matching compounds.

Examples

file <- system.file("extdata","sample1.cdf",package="gcxgclab")
frame <- extract_data(file,mod_t=.5)
peaks <- top_peaks(frame$TIC_df, 5)
mz <- find_ms(frame, t_peak=peaks$'T'[1])
masslist <- mass_list()
non_targeted(masslist, mz, THR=0.05)