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

## Documentation for package ‘MSnbase’ version 1.0.7

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

A C D E F H I L M N O P Q R S T 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
assayData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

## -- C --

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
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

## -- D --

description-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

## -- E --

experimentData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
expinfo-method | The "MIAPE" Class for Storing Proteomics Experiment Information
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
extractSpectra | Extracts a set of spectra from an 'MSnExp' object
extractSpectra-method | The 'MSnExp' Class for MS Data And Meta-Data
extractSpectra-methods | Extracts a set of spectra from an 'MSnExp' object

## -- F --

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

## -- 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 --

intensity | The "Spectrum" Class
intensity-method | The "Spectrum" Class
intensity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata
iTRAQ4 | iTRAQ 4-plex set
iTRAQ5 | iTRAQ 4-plex set
iTRAQ8 | iTRAQ 4-plex set
iTRAQ9 | iTRAQ 4-plex 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

## -- M --

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 --

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.
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

## -- 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 | Graphical overview of the 'MSnExp' object
plot2d-method | The 'MSnExp' Class for MS Data And Meta-Data
plot2d-method | Graphical overview of the 'MSnExp' object
plot2d-methods | Graphical overview of the 'MSnExp' object
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
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

## -- 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.
readMzXMLData | Import mzXML files as 'MSnExp' instances.
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
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
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 --

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
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

## -- 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

## -- misc --

[-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