# MSnbase: Base Functions and Classes for MS-based Proteomics

## Documentation for package ‘MSnbase’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H I L M N O P Q R S T U V W misc

MSnbase-package | MSnbase: Base Functions and Classes for MS-based Proteomics

## -- A --

abstract-method | The "MIAPE" Class for Storing Proteomics Experiment Information
abstract-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
acquisitionNum | The "Spectrum" Class
acquisitionNum-method | The "Spectrum" Class
acquisitionNum-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
analyser | The "MIAPE" Class for Storing Proteomics Experiment Information
analyser-method | The "MIAPE" Class for Storing Proteomics Experiment Information
analyser-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
analyser-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
analyserDetails | The "MIAPE" Class for Storing Proteomics Experiment Information
analyserDetails-method | The "MIAPE" Class for Storing Proteomics Experiment Information
analyserDetails-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
analyzer | The "MIAPE" Class for Storing Proteomics Experiment Information
analyzer-method | The "MIAPE" Class for Storing Proteomics Experiment Information
analyzer-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
analyzer-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
analyzerDetails | The "MIAPE" Class for Storing Proteomics Experiment Information
analyzerDetails-method | The "MIAPE" Class for Storing Proteomics Experiment Information
analyzerDetails-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
as.data.frame.Spectrum | The "Spectrum" Class
as.ExpressionSet.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
assayData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

## -- C --

centroided | The "Spectrum" Class
centroided-method | The "Spectrum" Class
centroided-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
centroided<- | The "Spectrum" Class
centroided<--method | The "Spectrum" Class
centroided<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
class:MIAPE | The "MIAPE" Class for Storing Proteomics Experiment Information
class:MSnExp | The 'MSnExp' Class for MS Data And Meta-Data
class:MSnProcess | The "MSnProcess" Class
class:MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
class:NAnnotatedDataFrame | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
class:pSet | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
class:ReporterIons | The "ReporterIons" Class
class:Spectrum | The "Spectrum" Class
class:Spectrum1 | The "Spectrum1" Class for MS1 Spectra
class:Spectrum2 | The "Spectrum2" Class for MSMS Spectra
clean | Cleans 'MSnExp' or 'Spectrum' instances
clean-method | The 'MSnExp' Class for MS Data And Meta-Data
clean-method | The "Spectrum" Class
clean-methods | Cleans 'MSnExp' or 'Spectrum' instances
coerce-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
coerce-method | The "Spectrum" Class
collisionEnergy | The "Spectrum2" Class for MSMS Spectra
collisionEnergy-method | The "Spectrum2" Class for MSMS Spectra
collisionEnergy-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
combine-method | The "MIAPE" Class for Storing Proteomics Experiment Information
combine-method | The "MSnProcess" Class
combine-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
combineFeatures | Combines features in an 'MSnSet' object

## -- D --

description-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
description-method | The "ReporterIons" Class
description-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
detectorType | The "MIAPE" Class for Storing Proteomics Experiment Information
detectorType-method | The "MIAPE" Class for Storing Proteomics Experiment Information
detectorType-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
detectorType-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
dim | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
dim-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
dim-method | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
dim-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
droplevels.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

## -- E --

expemail | The "MIAPE" Class for Storing Proteomics Experiment Information
expemail-method | The "MIAPE" Class for Storing Proteomics Experiment Information
expemail-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
expemail-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
experimentData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
experimentData<--method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
expinfo-method | The "MIAPE" Class for Storing Proteomics Experiment Information
exprsToRatios | Calculate all ratio pairs
exprsToRatios-method | Calculate all ratio pairs
exprsToRatios-methods | Calculate all ratio pairs
exptitle | The "MIAPE" Class for Storing Proteomics Experiment Information
exptitle-method | The "MIAPE" Class for Storing Proteomics Experiment Information
exptitle-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
exptitle-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
extractPrecSpectra | Extracts precursor-specific spectra from an 'MSnExp' object
extractPrecSpectra-method | The 'MSnExp' Class for MS Data And Meta-Data
extractPrecSpectra-methods | Extracts precursor-specific spectra from an 'MSnExp' object

## -- F --

fData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
featureCV | Calculates coeffivient of variation for features
featureData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
featureNames-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fileNames | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fileNames-method | The "MSnProcess" Class
fileNames-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
fileNames-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fillUp | Fills up a vector
filterNA | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
filterNA-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
formatRt | Format Retention Time
fromFile | The "Spectrum" Class
fromFile-method | The "Spectrum" Class
fromFile-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fvarLabels-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
fvarMetadata-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

## -- G --

getRatios | Calculate all ratio pairs
getVariableName | Return a variable name

## -- H --

header | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
header-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

## -- I --

image-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
impute | Quantitative proteomics data imputation
impute-method | Quantitative proteomics data imputation
impute-methods | Quantitative proteomics data imputation
instrumentCustomisations | The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentCustomisations-method | The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentCustomisations-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
instrumentManufacturer | The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentManufacturer-method | The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentManufacturer-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
instrumentModel | The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentModel-method | The "MIAPE" Class for Storing Proteomics Experiment Information
instrumentModel-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
intensity | The "Spectrum" Class
intensity-method | The "Spectrum" Class
intensity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
ionCount | The "Spectrum" Class
ionCount-method | The "Spectrum" Class
ionCount-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
ionSource | The "MIAPE" Class for Storing Proteomics Experiment Information
ionSource-method | The "MIAPE" Class for Storing Proteomics Experiment Information
ionSource-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
ionSource-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
ionSourceDetails | The "MIAPE" Class for Storing Proteomics Experiment Information
ionSourceDetails-method | The "MIAPE" Class for Storing Proteomics Experiment Information
ionSourceDetails-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
is.na.MSnSet | Exploring missing data in 'MSnSet' instances
iTRAQ4 | iTRAQ 4-plex set
iTRAQ5 | iTRAQ 4-plex set
iTRAQ8 | iTRAQ 4-plex set
iTRAQ9 | iTRAQ 4-plex set
itraqdata | Example 'MSnExp' data set

## -- L --

length | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
length-method | The "ReporterIons" Class
length-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
log-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

## -- M --

makeImpuritiesMatrix | Performs reporter ions purity correction
makeMTD | Creates the mzTab metadata section
makePEP | Creates the mzTab peptide section
makePRT | Creates the mzTab protein section
MAplot-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
meanSdPlot-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
MIAPE | The "MIAPE" Class for Storing Proteomics Experiment Information
MIAPE-class | The "MIAPE" Class for Storing Proteomics Experiment Information
msInfo | The "MIAPE" Class for Storing Proteomics Experiment Information
msInfo-method | The "MIAPE" Class for Storing Proteomics Experiment Information
msInfo-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
msInfo-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
msLevel | The "Spectrum" Class
msLevel-method | The "Spectrum" Class
msLevel-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
MSnbase | MSnbase: Base Functions and Classes for MS-based Proteomics
MSnExp | The 'MSnExp' Class for MS Data And Meta-Data
MSnExp-class | The 'MSnExp' Class for MS Data And Meta-Data
MSnProcess | The "MSnProcess" Class
MSnProcess-class | The "MSnProcess" Class
MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
MSnSet-class | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
multiLabels | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
multiLabels-method | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
multiplex | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
multiplex-method | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
mz | The "Spectrum" Class
mz-method | The "ReporterIons" Class
mz-method | The "Spectrum" Class
mz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

## -- N --

names-method | The "ReporterIons" Class
NAnnotatedDataFrame | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
NAnnotatedDataFrame-class | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
normalise | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalise-method | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalise-methods | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalize | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalize-method | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
normalize-methods | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
notes-method | The "MIAPE" Class for Storing Proteomics Experiment Information
notes-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
notes<--method | The "MIAPE" Class for Storing Proteomics Experiment Information
nQuants | Count the number of quantitfied features.

## -- O --

otherInfo-method | The "MIAPE" Class for Storing Proteomics Experiment Information

## -- P --

pData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
peaksCount | The "Spectrum" Class
peaksCount-method | The "Spectrum" Class
peaksCount-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
phenoData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
plot | Plotting 'Spectrum' object(s)
plot,MSnExp | The 'MSnExp' Class for MS Data And Meta-Data
plot-method | The 'MSnExp' Class for MS Data And Meta-Data
plot-method | The "Spectrum" Class
plot-methods | Plotting 'Spectrum' object(s)
plot.MSnExp | Plotting 'Spectrum' object(s)
plot.Spectrum | Plotting 'Spectrum' object(s)
plot2d | The 'plot2d' method for 'MSnExp' quality assessment
plot2d-method | The 'plot2d' method for 'MSnExp' quality assessment
plot2d-methods | The 'plot2d' method for 'MSnExp' quality assessment
plotDensity | The 'plotDensity' method for 'MSnExp' quality assessment
plotDensity-method | The 'plotDensity' method for 'MSnExp' quality assessment
plotDensity-methods | The 'plotDensity' method for 'MSnExp' quality assessment
plotMzDelta | The delta m/z plot for 'MSnExp' quality assessment
plotMzDelta-method | The delta m/z plot for 'MSnExp' quality assessment
plotMzDelta-methods | The delta m/z plot for 'MSnExp' quality assessment
plotNA | Exploring missing data in 'MSnSet' instances
plotNA-method | Exploring missing data in 'MSnSet' instances
plotNA-methods | Exploring missing data in 'MSnSet' instances
polarity | The "Spectrum1" Class for MS1 Spectra
polarity-method | The "Spectrum1" Class for MS1 Spectra
polarity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precAcquisitionNum | The "Spectrum2" Class for MSMS Spectra
precAcquisitionNum-method | The "Spectrum2" Class for MSMS Spectra
precAcquisitionNum-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precScanNum | The "Spectrum2" Class for MSMS Spectra
precScanNum-method | The "Spectrum2" Class for MSMS Spectra
precScanNum-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precSelection | Number of precursor selection events
precSelectionTable | Number of precursor selection events
precursorCharge | The "Spectrum2" Class for MSMS Spectra
precursorCharge-method | The "Spectrum2" Class for MSMS Spectra
precursorCharge-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precursorIntensity | The "Spectrum2" Class for MSMS Spectra
precursorIntensity-method | The "Spectrum2" Class for MSMS Spectra
precursorIntensity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
precursorMz | The "Spectrum2" Class for MSMS Spectra
precursorMz-method | The "Spectrum2" Class for MSMS Spectra
precursorMz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
processingData | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
processingData-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
processingData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
protocolData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
pSet | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
pSet-class | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
pubMedIds-method | The "MIAPE" Class for Storing Proteomics Experiment Information
pubMedIds-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
pubMedIds<--method | The "MIAPE" Class for Storing Proteomics Experiment Information
purityCorrect | Performs reporter ions purity correction
purityCorrect-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
purityCorrect-methods | Performs reporter ions purity correction

## -- Q --

qual | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
qual-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
quantify | Quantifies 'MSnExp' and 'Spectrum' objects
quantify-method | The 'MSnExp' Class for MS Data And Meta-Data
quantify-method | The "Spectrum" Class
quantify-methods | Quantifies 'MSnExp' and 'Spectrum' objects

## -- R --

readIspyData | Reads an ispy2 result spread sheet and creates a fully featured 'MSnSet' instance.
readMgfData | Import mgf files as 'MSnExp' instances.
readMSData | Imports mass-spectrometry raw data files as 'MSnExp' instances.
readMSnSet | Read 'MSnSet'
readMzTabData | Read an 'mzTab' file
removePeaks | Removes low intensity peaks
removePeaks-method | The 'MSnExp' Class for MS Data And Meta-Data
removePeaks-method | The "Spectrum" Class
removePeaks-methods | Removes low intensity peaks
removeReporters | Removes reporter ion tag peaks
removeReporters-method | The 'MSnExp' Class for MS Data And Meta-Data
removeReporters-method | The "Spectrum2" Class for MSMS Spectra
removeReporters-methods | Removes reporter ion tag peaks
reporterColors | The "ReporterIons" Class
reporterColors-method | The "ReporterIons" Class
reporterColours | The "ReporterIons" Class
reporterColours-method | The "ReporterIons" Class
ReporterIons | The "ReporterIons" Class
ReporterIons-class | The "ReporterIons" Class
reporterNames | The "ReporterIons" Class
reporterNames-method | The "ReporterIons" Class
reporterNames<- | The "ReporterIons" Class
reporterNames<--method | The "ReporterIons" Class
rtime | The "Spectrum" Class
rtime-method | The "Spectrum" Class
rtime-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

## -- S --

sampleNames-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
samples-method | The "MIAPE" Class for Storing Proteomics Experiment Information
scale-method | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects
scanIndex | The "Spectrum" Class
scanIndex-method | The "Spectrum" Class
scanIndex-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
show-method | The "MIAPE" Class for Storing Proteomics Experiment Information
show-method | The 'MSnExp' Class for MS Data And Meta-Data
show-method | The "MSnProcess" Class
show-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
show-method | Class Containing Measured Variables and Their Meta-Data Description for Multiplexed Experiments.
show-method | The "ReporterIons" Class
show-method | The "Spectrum" Class
spectra | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
spectra-method | The 'MSnExp' Class for MS Data And Meta-Data
spectra-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
Spectrum | The "Spectrum" Class
Spectrum-class | The "Spectrum" Class
Spectrum1 | The "Spectrum1" Class for MS1 Spectra
Spectrum1-class | The "Spectrum1" Class for MS1 Spectra
Spectrum2 | The "Spectrum2" Class for MSMS Spectra
Spectrum2-class | The "Spectrum2" Class for MSMS Spectra

## -- T --

t.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
tic | The "Spectrum" Class
tic-method | The "Spectrum" Class
tic-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
TMT6 | TMT 6-plex set
TMT7 | TMT 6-plex set
topN | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
topN-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
trimMz | Trims 'MSnExp' or 'Spectrum' instances
trimMz-method | The 'MSnExp' Class for MS Data And Meta-Data
trimMz-method | The "Spectrum" Class
trimMz-methods | Trims 'MSnExp' or 'Spectrum' instances

## -- U --

updateFeatureNames | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
updateFvarLabels | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
updateSampleNames | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

## -- V --

varLabels-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
varMetadata-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

## -- W --

width | The "ReporterIons" Class
width-method | The "ReporterIons" Class
write.exprs | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
write.exprs-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
writeMgfData | Write an experiment or spectrum to an mgf file
writeMgfData-method | Write an experiment or spectrum to an mgf file
writeMgfData-methods | Write an experiment or spectrum to an mgf file
writeMzTabData | Writes an 'MSnSet' to an mzTab file

## -- misc --

[-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
[-method | The "ReporterIons" Class
[-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
[[-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata