exptable: Sample table for the generation of a database of standards...

In yguitton/metaMS: MS-based metabolomics annotation pipeline

Sample table for the generation of a database of standards (LCMS)

Description

An example of a table used to construct a database of standards. This particular table is used to obtain object LCDBtest.

Usage

data(exptable)

Format

exptable is a data.frame summarizing information on the chemical standards used for creating a database.

Column description:

ChemSpiderID

The Chemspider ID of a specific compound.

compound

A string containing the (human) readable name of the compound.

formula

The formula of the compound.

M.ref

The theoretical value for the observed m/z reference ion. This can be, for example, the protonated (de-protonated) molecular ion, a known adduct or a characteristic fragment.

mz.observed

The manually validated m/z value of the reference ion.

RTman

The manually validated retention time value for the standard.

stdFile

The name (including the path) of the raw data file of the standard.

Details

Mandatory fields are: ChemSpiderID, mz.observed, RTman, and stdFile.

In the current implementation the M.ref value is not used in the creation of the DB. The difference between M.ref and m.observed, however, could be used to construct the mass error surface used during feature annotation.

The sample table is also an element (Reftable) of the LCDB list generated by createSTDdbLC.

Author(s)

Pietro Franceschi

See Also

createSTDdbLC

yguitton/metaMS documentation built on Feb. 27, 2023, 11:45 p.m.