mz_iso_quant: Calculate isotope abundances

Description Usage Arguments Value Examples

View source: R/mz_iso_quant.R

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

1
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

1
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.