findMz: Find compound information

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Retrieves compound information from the loaded compound list or calculates it from the SMILES code in the list.

Usage

findMz(cpdID, mode = "pH", ppm = 10, deltaMz = 0, retrieval="standard")

findRt(cpdID) 

findSmiles(cpdID) 

findFormula(cpdID, retrieval="standard") 

findCAS(cpdID)

findName(cpdID)

findLevel(cpdID, compact=FALSE)

Arguments

cpdID	The compound ID in the compound list.
mode	Specifies the species of the molecule: An empty string specifies uncharged monoisotopic mass, pH (positive H) specifies [M+H]+, pNa specifies [M+Na]+, pM specifies [M]+, mH and mFA specify [M-H]- and [M+FA]-, respectively. (I apologize for the naming of pH which has absolutely nothing to do with chemical pH values.)
ppm	Specifies ppm window (10 ppm will return the range of the molecular mass + and - 10 ppm).
deltaMz	Specifies additional m/z window to add to the range (deltaMz = 0.02 will return the range of the molecular mass +- 0.02 (and additionally +- the set ppm value).
retrieval	A value that determines whether the files should be handled either as "standard", if the compoundlist is complete, "tentative", if at least a formula is present or "unknown" if the only know thing is the m/z
compact	Only for findLevel, returns the "retrieval" parameter used for many functions within RMassBank if TRUE

Value

findMz will return a list(mzCenter=, mzMin=, mzMax=) with the molecular weight of the given ion, as calculated from the SMILES code and Rcdk.

findRt, findSmiles,findCAS,findName will return the corresponding entry from the compound list. findFormula returns the molecular formula as determined from the SMILES code.

Author(s)

Michael Stravs

See Also

findMass, loadList, findMz.formula

Examples

## Not run: %
	findMz(123, "pH", 5)
	findFormula(123)

## End(Not run)

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.