threeStdsDB: Information on three chemical standards measured in GC-MS...

In metaMS: MS-based metabolomics annotation pipeline

Description

User information needed to build up an in-house database, the external database for cross-checking mass spectra, and the final database obtained with createSTDdbGC for three chemical standards.

Usage

data(threeStdsDB)
data(threeStdsInfo)
data(threeStdsNIST)

Details

Raw GC-MS data for the three standards, linalool, methyl salicylate and ethyl hexanoate, are available in package metaMSdata. Manual information required to build up an in-house database should be presented in the form of a data.frame, an example of which is stdInfo. Presenting this information to createSTDdbGC leads to processing of the raw data, and cross-checking with an external database containing mass spectra. An excerpt of the NIST database, containing only spectra for these three compounds, is available in smallDB. The final database that is then obtained can be inspected in object DB, which is a simple list of tags and values. For use as a reference database, several of these fields are mandatory. Currently these are Name, monoMW, pspectrum and std.rt.

Source

Georg Weingart

Examples

data(threeStdsNIST)
length(smallDB)

data(threeStdsInfo)
stdInfo

data(threeStdsDB)
par(mfrow = c(3,1))
sapply(DB, function(x) plotPseudoSpectrum(x$pspectrum, main = x$Name))

metaMS documentation built on Nov. 8, 2020, 8:21 p.m.