mz_iso_quant: Calculate isotope abundances

In wmoldham/mzrtools: Make Molecular Formulas Useful for Mass Spectrometry Applications

Description

mz_iso_quant will calculate the probability matrix given a molecular formula, scan polarity, and tracer element with its isotopic purity. This function identifies and aggregates probabilities for isotopes that are not resolved from the labeled isotopes of interest.

Usage

mz_iso_quant(molecule, polarity = "negative", tracer = "C", purity = NULL, ...)

Arguments

molecule	A string containing a molecular formula (e.g., "C2H7NO3S"). Structural formulas containing parentheses are not acceptable. Charges may be included, but the charge count should follow the sign (e.g., "C10H16N5O13P3-3").
polarity	Type of m/z to return. Accepts one of "neutral", which returns the monoisotopic mass; "positive", which returns the [M+H]+ mass; or "negative", which returns the [M-H]- mass.
tracer	A vector of elements labeled by the tracer.
purity	A named list defining tracer isotope enrichment purity where, for example, C = 0.99 indicates 99% C13 enrichment for each labeled carbon. This argument does not adjust for global tracer dilution, however.
...	Passes the arguments nominal_resolution (default 70,000) and nominal_mz (default 200) used to determine the delta m/z below which peaks are considered unresolved.

Value

A list containing a probability matrix of isotope targets and the output of mz_iso_annotate.

Examples

mz_iso_quant("C3H4O3", tracer = c("C", "H"), purity = list(C = 0.98, H = 1))

wmoldham/mzrtools documentation built on Oct. 26, 2020, 2:40 p.m.