Information on three chemical standards measured in GC-MS (liquid injection)

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))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(metaMS)
Loading required package: CAMERA
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: xcms
Loading required package: mzR
Loading required package: Rcpp
Loading required package: ProtGenerics

Attaching package: 'xcms'

The following objects are masked from 'package:Biobase':

    phenoData, phenoData<-

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/metaMS/threeStdsDB.Rd_%03d_medium.png", width=480, height=480)
> ### Name: threeStdsDB
> ### Title: Information on three chemical standards measured in GC-MS
> ###   (liquid injection)
> ### Aliases: threeStdsInfo stdInfo threeStdsDB DB threeStdsNIST smallDB
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(threeStdsNIST)
> length(smallDB)
[1] 78
> 
> data(threeStdsInfo)
> stdInfo
     CAS              Name RTman ChemspiderID              SMILES
1  78706          Linalool 17.86     13849981 CC(=CCCC(C)(C=C)O)C
2 119368 Methyl salicylate 22.44     13848808    O=C(OC)c1ccccc1O
3 123660   Ethyl hexanoate 10.77        29005       O=C(OCC)CCCCC
                                                      InChI
1 1/C10H18O/c1-5-10(4,11)8-6-7-9(2)3/h5,7,11H,1,6,8H2,2-4H3
2           1/C8H8O3/c1-11-8(10)6-4-2-3-5-7(6)9/h2-5,9H,1H3
3              1/C8H16O2/c1-3-5-6-7-8(9)10-4-2/h3-7H2,1-2H3
                                              csLinks   monoMW stdFile
1 www.chemspider.com/Chemical-Structure.13849981.html 154.1358    <NA>
2 www.chemspider.com/Chemical-Structure.13848808.html 152.0473    <NA>
3    www.chemspider.com/Chemical-Structure.29005.html 144.1150    <NA>
> 
> data(threeStdsDB)
> par(mfrow = c(3,1))
> sapply(DB, function(x) plotPseudoSpectrum(x$pspectrum, main = x$Name))
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>