isobar (version 1.18.0)

IBSpectra-class: IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data

Description

This class represents a quantitative MS proteomics experiment labeled using Isobaric tags (iTRAQ, TMT). IBSpectra is a abstract class which is implemented in the IBSpectraTypes classes iTRAQ4plexSpectra, iTRAQ8plexSpectra, TMT2plexSpectra, TMT6plexSpectra and TMT10plexSpectra. It contains per-spectrum meassurements of the reporter tag intensity and m/z in assayData, and protein grouping in proteinGroup.

Objects from the Class

IBSpectra objects are typically created using the readIBSpectra method or by calls of the form new("iTRAQ4plexSpectra",data=NULL,data.ions=NULL,...).

Slots

IBSpectra extends eSet which is a container for high-throughput assays and experimental metadata. Slots introduced in eSet (for more details on slots and methods refer to eSet help):

assayData:

Contains matrices 'ions' and 'mass storing reporter tag intensities and m/z values for each tag and spectrum. Can be accessed by reporterIntensities and reporterMasses. Class: AssayData

phenoData:

Contains experimenter-supplied variables describing phenotypes behind reporter tags. Class: AnnotatedDataFrame-class

featureData:

Describes the spectra's retention time, charge, peptide sequence, etc and can be accessed by fData. Class: AnnotatedDataFrame

experimentData:

Contains details of experimental methods. Class: MIAME

annotation:

UNUSED. Label associated with the annotation package used in the experiment. Class: character

protocolData:

UNUSED. Contains equipment-generated variables describing reporter tags. Class: AnnotatedDataFrame

log:

character matrix logging isotope impurity correction, normalization, etc.

Slots introduced in IBSpectra:

proteinGroup:

A ProteinGroup object describing peptide and protein identifications grouped by shared peptides.

reporterTagNames:

A character vector denoting the reporter tag labels.

reporterMasses:

The 'true' m/z of the reporter tags in the MS/MS spectrum, used to isolate m/z-intensity pairs from peaklist.

isotopeImpurities:

Manufacturer supplied isotope impurities, need to be set per batch and used for correction by correctIsotopeImpurities.

Constructor

See readIBSpectra for creation based on peaklist (e.g. MGF format) and identification files (Mascot and Phenyx output).

new(type,data):

Creates a IBSpectra object.

type

Denotes the type of IBSpectra, either 'iTRAQ4plexSpectra','iTRAQ8plexSpectra','TMT2plexSpectra', 'TMT6plexSpectra' or 'TMT10plexSpectra'. Call IBSpectraTypes() to see a list of the implemented types.

data

A 'data.frame' in a ibspectra-csv format.

Coercion

In the code snippets below, x is a IBSpectra object. IBSpectra object can be coerced to

as(x, "data.frame"):

Creates a data.frame containing all identification and quantitation information. Peptide matching to multiple proteins produce multiple lines.

ibSpectra.as.concise.data.frame(x):

Creates a data.frame containing all identification and quantitation information. Proteins are concatenated - so the resulting data.frame has one line per spectrum.

as(x, "MSnSet"):

Coerces to a MSnSet object (package MSnbase).

as(msnset,"IBSpectra"):

Coerces a MSnSet to IBSpectra object.

Accessors

In the following code snippets, x is a IBSpectra object.

proteinGroup(x):

Gets and sets the ProteinGroup.

isotopeImpurities(x):

Gets and sets the isotope impurities of the isobaric tags as defined by the manufacturers per batch.

reporterData(x,element="ions",na.rm=FALSE,na.rm.f='any',...):

Gets and sets the element ('ions' or 'mass') for each tag and spectrum. '...' is handed down to spectrumSel, so it is possible to select for peptides or proteins. If na.rm is TRUE, than spectra missing quantitative information in 'any' or 'all' channels (parameter na.rm.f) are removed.

reporterIntensities(x,...):

Convenience function, calls reporterData(...,element="ions")

reporterMasses(x,...):

Convenience function, calls reporterData(...,element="mass")

spectrumTitles(x,...):

Gets the spectrum titles. '...' is passed down to spectrumSel.

classLabels(x):

Gets and sets the class labels in phenoData. Used for summarization, see also estimateRatio and phenoData.

Methods

In the following code snippets, x is a IBSpectra object.

subsetIBSpectra(x, protein=NULL, peptide=NULL, direction="exclude",specificity):

Get a 'subset' of IBSpectra: include or exclude proteins or peptides. When selection is based on proteins, it can be defined to exclude only peptides which are specific to the protein ('reporter-specific'), specific to the group ('group-specific') or which are shared with other proteins ('unspecific'). See subsetIBSpectra.

spectrumSel(x,peptide,protein,specificity="reporter-specific"):

Gets a boolean vector selecting the corresponding spectra: If peptide is given, all spectra assigned to this peptide. If protein is given, all spectra assigned to peptides of this protein with specificity 'specificity'. See also ProteinGroup.

See Also

ProteinGroup, isobar-preprocessing, isobar-analysis, isobar-plots

Examples

data(ibspiked_set1)
ibspiked_set1
head(reporterIntensities(ibspiked_set1))
head(reporterMasses(ibspiked_set1))
proteinGroup(ibspiked_set1)
isotopeImpurities(ibspiked_set1)

# create new object
set.seed(123)
data <- data.frame(spectrum=letters,
                   peptide=sample(c("pepA","pepB","pepC"),26,TRUE),
                   start.pos=1,
                   modif=sample(c("::X:::",":Y::::","::Z:::"),26,TRUE),
                   accession=c("protein1","protein2"))
data.ions <- matrix(rnorm(26*2,1000,50),
                    ncol=2,dimnames=list(letters,NULL))
data.mass <- matrix(rep(c(126.1,127.1),26),
                    ncol=2,byrow=TRUE,dimnames=list(letters,NULL))
ib <- new("TMT2plexSpectra",data,data.ions,data.mass)
ib
reporterIntensities(ib)
isotopeImpurities(ib) <- matrix(c(0.8,0.1,0.2,0.9),nrow=2)
reporterIntensities(correctIsotopeImpurities(ib))