InterpretTP {InterpretMSSpectrum}

InterpretTP.

Description

InterpretTP is a wrapper function around InterpretMSSpectrum which will read, evaluate and plot a deconvoluted mass spectrum (mass*intensity pairs) from either TMS-derivatized GC-APCI-MS data or ESI+/- data. It allows to provide a chemical formula as a potential precursor of the spectrum. This formula will be used to set the parameters 'allowed_elements' and 'maxElements' during de-novo formula generation.

Usage

InterpretTP(fml = NULL, param = "APCIpos", ...)

Arguments

fml

A chemical formula of the standard used for transformation product generation.

param

Keyword or parameter list, similar as in InterpretMSSpectrum.

...

Arguments passed on to InterpretMSSpectrum

spec

A 2-column matrix of mz/int pairs. If spec=NULL then InterpretMSSpectrum tries to read data from clipboard (i.e. two columns copied from an Excel spreadsheet).

precursor

The ion (m/z) from spec closest to this mass will be considered as precursor (can be nominal, i.e. if precursor=364 then 364.1234 would be selected from spectrum if it is closest).

correct_peak

For testing purposes. A character in the form of "name, formula, mz" to evaluate spectra against. Note! Separating character is ', '.

met_db

A metabolite DB (e.g. GMD or internal) can be provided to search for candidates comparing M+H ions (cf. Examples).

typical_losses_definition

A file name (e.g. D:/BuildingBlocks_GCAPCI.txt) from where to load relevant neutral losses (cf. Details). Alternatively an data frame with columns 'Name', 'Formula' and 'Mass'.

silent

Logical. If TRUE no plot is generated and no output except final candidate list is returned.

dppm

Specifies ppm error for Rdisop formula calculation.

formula_db

A pre calculated database of sum formulas and their isotopic fine structures can be used to extremely speed up the function.

Details

For further details refer to InterpretMSSpectrum.

Value

An annotated plot of the mass spectrum and detailed information within the console. Main result, list of final candidate formulas and their putative fragments, will be returned invisibly.

Examples

# load test data
utils::data(apci_spectrum)

# provide information of a correct peak (if you know) as character
cp <- "Glutamic acid (3TMS), C14H33NO4Si3, 364.1790"

# provide database of known peaks and correct peak
mdb <- data.frame(
  "Name" = c("Glutamic acid (3TMS)", "other peak with same sum formula"),
  "Formula" = c("C14H33NO4Si3", "C14H33NO4Si3"),
  "M+H" = c(364.179, 364.179), stringsAsFactors = FALSE, check.names = FALSE
)

# provide a database of precalculated formulas to speed up the process
fdb <- system.file("extdata", "APCI_min.db", package = "InterpretMSSpectrum")

# apply function providing above arguments (dppm is set to 0.5 to reduce run time)
InterpretTP(fml = "C14H33NO4Si3", spec=apci_spectrum, param="APCIpos")