calcMF: calcMF
In mjhelf/MassTools: R package for mass and molecular formula calculations

Description Usage Arguments Details Value References Examples

View source: R/Functions_MF_prediction.R

Calculate molecular formulas from a monoisotopic mass. This function uses Rdisop to generate molecular formulas, and can apply many of the filters described as the "seven golden rules"[1]

calcMF(mz = 200.000659, z = 1, ppm = 5, top = NULL,
  elements = Rdisop::initializeCHNOPS(), maxCounts = TRUE,
  SeniorRule = TRUE, HCratio = TRUE, moreRatios = TRUE,
  elementHeuristic = TRUE, Filters = list(DBErange = c(-5, 40),
  minElements = "C0", maxElements = "C99999", parity = "e", maxCounts =
  TRUE, SENIOR3 = 0, HCratio = TRUE, moreRatios = TRUE, elementHeuristic =
  TRUE), summarize = FALSE, BPPARAM = NULL)

`mz`	monoisotopic mass or monoisotopic m/z value
`z`	charge (set 0 for uncharged)
`ppm`	error tolerance in ppm
`top`	if not NULL, maximum number of `top` formulas to be returned, as ranked by ppm error
`elements`	either NULL or an element list for Rdisop, as generated by initializeCHNOPS and related functions.
`maxCounts`	check each predicted molecula formula for maximum number of elements expected in a natural product of its size ("Golden Rule #1")
`SeniorRule`	for each predicted molecula formula, calculate the sum of valences minus twice (the number of atoms minus 1) (to check for Senior's third theorem, "Golden Rule #2")[1][2][3]
`HCratio`	for each predicted molecula formula, calculate Hydrogen/ Carbon count ratio ("Golden Rule #4")
`moreRatios`	for each predicted molecula formula, calculate Nitrogen/Carbon, Oxygen/Carbon, Phosphorus/Carbon and Sulfur/Carbon count ratios ("Golden Rule #5")
`elementHeuristic`	apply a heuristic HNOPS probability check as proposed in "Golden Rule #6"
`Filters`	which filters to apply, see Details
`summarize`	if `TRUE`, will return a single character string with molecular formulas and charge instead of a data.table
`BPPARAM`	parameters for parallel processing with BiocParallel. Can be bpparam(), or an object of these classes SnowParam-class, MulticoreParam-class. If NULL, SerialParam() is called (no multicore processing).

Filters

These filtering steps can be selected. Filter items that are NULL (or not in the list) will not be applied.

DBErange: numeric vector of length 2, defining lower and upper limit for double bond equivalents in the molecule
minElements: character(1) with a molecula formula defining the minimum number of atom counts for a set of elements
maxElements: character(1) with a molecula formula defining the maximum number of atom counts for a set of elements
parity: filter for parity. must be "e" (for even) or "o" (for odd). What to expect depends on ionization technique used.
maxCounts: if TRUE, uses a filter limiting atom counts for elements as described by Kind & Fiehn [1]
SENIOR3: If TRUE, the sum of valences has to be greater than or equal to twice the number of atoms minus 1, as Senior's third theorem suggests [1][2][3]
HCratio: If TRUE, molecular formulas must have a Hydrogen/ Carbon count ratio of >0.2 and <3.1 ("Golden Rule #4")[1]. Will be ignored if no Hydrogen or Carbon present in a molecule.
moreRatios: If TRUE, molecular formulas must have these atom count ratios: Nitrogen/Carbon <1.3, Oxygen/Carbon <1.2, Phosphorus/Carbon <0.3 and Sulfur/Carbon <0.8 ("Golden Rule #5")[1]. Will be ignored if no Carbon present in a molecule.
elementHeuristic: If TRUE, additional element ratio heuristic is applied ("Golden Rule #6") [1]

a data.frame (or list of data.frames if multiple mz values are supplied) with molecular formulas generated with decomposeMass() with additional information and optionally filtered as described. NOTE: If summarize = TRUE, results for each query mz value are summarized in a single character string with all molecular formulas matching filter criteria

Kind T, Fiehn O (2007) Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 8:105. doi: 10.1186/1471-2105-8-105
Senior JK (1951) Partitions and Their Representative Graphs. Am J Math 73:663. doi: 10.2307/2372318
Morikawa T, Newbold BT (2003) Analogous odd-even parities in mathematics and chemistry. Chemistry 12:445–450