findMass: Calculate exact mass

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

Description

Retrieves the exact mass of the uncharged molecule. It works directly from the SMILES and therefore is used in the MassBank workflow (mbWorkflow) - there, all properties are calculated from the SMILES code retrieved from the database. (Alternatively, takes also the compound ID as parameter and looks it up.) Calculation relies on Rcdk.

Usage

findMass(cpdID_or_smiles, retrieval = "standard", mode = "pH")

Arguments

cpdID_or_smiles	SMILES code or compound ID of the molecule. (Numerics are treated as compound ID).
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
mode	"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA" for different ions ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-). Only needed for retrieval="unknown"

Value

Returns the exact mass of the uncharged molecule.

Author(s)

Michael Stravs

See Also

findMz

Examples

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findMass("OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O")

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