itraqdata is and example data sets is an iTRAQ 4-plex
experiment that has been run on an Orbitrap Velos instrument. It
includes identification data in the feature data slot obtain from the
Mascot search engine. It is a subset of an spike-in experiment where
proteins have spiked in an Erwinia background, as described in
Karp et al. (2010), Addressing accuracy and precision issues in
iTRAQ quantitation, Mol Cell Proteomics. 2010 Sep;9(9):1885-97. Epub
2010 Apr 10. (PMID 20382981).
The spiked-in proteins in itradata are BSA and ENO and are
present in relative abundances 1, 2.5, 5, 10 and 10, 5, 2.5, 1 in the
114, 115, 116 and 117 reporter tags.
The msnset object is produced by running the quantify
method on the itraqdata experimental data, as detailed in the
quantify example. This example data set is used in the
MSnbase-demo vignette, available with vignette("MSnbase-demo",
package="MSnbase").
The msnset2 object is another example iTRAQ4 data that is used
to demonstrate features of the package, in particular the iPQF
feature aggregation method, described in iPQF. It
corresponds to 11 proteins with spectra measurements from the original
data set described by Breitwieser et al. (2011) General
statistical modeling of data from protein relative expression isobaric
tags. J. Proteome Res., 10, 2758-2766.
Usage
itraqdata
Examples
data(itraqdata)
itraqdata
## created by
## msnset <- quantify(itraqdata, method = "trap", reporters = iTRAQ4)
data(msnset)
msnset
data(msnset2)
msnset2
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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Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MSnbase)
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 1.20.7
Read '?MSnbase' and references therein for information
about the package and how to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MSnbase/itraqdata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: itraqdata
> ### Title: Example 'MSnExp' and 'MSnSet' data sets
> ### Aliases: itraqdata itraqdata msnset msnset2
> ### Keywords: datasets
>
> ### ** Examples
>
> data(itraqdata)
> itraqdata
Object of class "MSnExp"
Object size in memory: 1.88 Mb
- - - Spectra data - - -
MS level(s): 2
Number of MS1 acquisitions: 1
Number of MSn scans: 55
Number of precursor ions: 55
55 unique MZs
Precursor MZ's: 401.74 - 1236.1
MSn M/Z range: 100 2069.27
MSn retention times: 19:9 - 50:18 minutes
- - - Processing information - - -
Data loaded: Wed May 11 18:54:39 2011
MSnbase version: 1.1.22
- - - Meta data - - -
phenoData
rowNames: 1
varLabels: sampleNames sampleNumbers
varMetadata: labelDescription
Loaded from:
dummyiTRAQ.mzXML
protocolData: none
featureData
featureNames: X1 X10 ... X9 (55 total)
fvarLabels: spectrum ProteinAccession ProteinDescription
PeptideSequence
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
>
> ## created by
> ## msnset <- quantify(itraqdata, method = "trap", reporters = iTRAQ4)
> data(msnset)
> msnset
MSnSet (storageMode: lockedEnvironment)
assayData: 55 features, 4 samples
element names: exprs
protocolData: none
phenoData
sampleNames: iTRAQ4.114 iTRAQ4.115 iTRAQ4.116 iTRAQ4.117
varLabels: mz reporters
varMetadata: labelDescription
featureData
featureNames: X1 X10 ... X9 (55 total)
fvarLabels: spectrum ProteinAccession ... collision.energy (15 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: No annotation
- - - Processing information - - -
Data loaded: Wed May 11 18:54:39 2011
iTRAQ4 quantification by trapezoidation: Wed Apr 1 21:41:53 2015
MSnbase version: 1.1.22
>
> data(msnset2)
> msnset2
MSnSet (storageMode: lockedEnvironment)
assayData: 614 features, 4 samples
element names: exprs
protocolData: none
phenoData: none
featureData
featureNames: 11695 11696 ... 390 (614 total)
fvarLabels: accession sequence ... rudist.org (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
- - - Processing information - - -
Subset [13758,4][614,4] Mon Jun 15 21:03:40 2015
MSnbase version: 1.14.1
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.