MS Data Analysis

Description Objects from the Class Slots Methods Note Author(s) References See Also

This class handles processing and visualization of the raw data from a single LC/MS or GS/MS run. It includes methods for producing a standard suite of plots including individual spectra, multi-scan average spectra, TIC, and EIC. It will also produce a feature list of significant peaks using matched filtration.

Objects can be created with the xcmsRaw constructor which reads data from a NetCDF file into a new object.

acquisitionNum:: Numeric representing the acquisition number of the individual scans/spectra. Length of acquisitionNum is equal to the number of spectra/scans in the object and hence equal to the scantime slot. Note however that this information is only available in mzML files.
env:: environment with three variables: mz - concatenated m/z values for all scans, intensity - corresponding signal intensity for each m/z value, and profile - matrix represention of the intensity values with columns representing scans and rows representing equally spaced m/z values. The profile matrix should be extracted with the profMat method.
filepath:: Path to the raw data file
gradient:: matrix with first row, time, containing the time point for interpolation and successive columns representing solvent fractions at each point
msnAcquisitionNum:: for each scan a unique acquisition number as reported via "spectrum id" (mzData) or "<scan num=...>" and "<scanOrigin num=...>" (mzXML)
msnCollisionEnergy:: "CollisionEnergy" (mzData) or "collisionEnergy" (mzXML)
msnLevel:: for each scan the "msLevel" (both mzData and mzXML)

msnPrecursorCharge:: "ChargeState" (mzData) and "precursorCharge" (mzXML)
msnPrecursorIntensity:: "Intensity" (mzData) or "precursorIntensity" (mzXML)
msnPrecursorMz:: "MassToChargeRatio" (mzData) or "precursorMz" (mzXML)
msnPrecursorScan:: "spectrumRef" (both mzData and mzXML)
msnRt:: Retention time of the scan
msnScanindex:: msnScanindex
mzrange:: numeric vector of length 2 with minimum and maximum m/z values represented in the profile matrix
polarity:: polarity
profmethod:: characer value with name of method used for generating the profile matrix.
profparam:: list to store additional profile matrix generation settings. Use the profinfo method to extract all profile matrix creation relevant information.
scanindex:: integer vector with starting positions of each scan in the mz and intensity variables (note that index values are based off a 0 initial position instead of 1).
scantime:: numeric vector with acquisition time (in seconds) for each scan.
tic:: numeric vector with total ion count (intensity) for each scan
mslevel:: Numeric representing the MS level that is present in MS1 slot. This slot should be accessed through its getter method mslevel.
scanrange:: Numeric of length 2 specifying the scan range (or NULL for the full range). This slot should be accessed through its getter method scanrange. Note that the scanrange will always be 1 to the number of scans within the xcmsRaw object, which does not necessarily have to match to the scan index in the original mzML file (e.g. if the original data was sub-setted). The acquisitionNum information can be used to track the original position of each scan in the mzML file.

findPeaks: signature(object = "xcmsRaw"): feature detection using matched filtration in the chromatographic time domain
getEIC: signature(object = "xcmsRaw"): get extracted ion chromatograms in specified m/z ranges. This will return the total ion chromatogram (TIC) if the m/z range corresponds to the full m/z range (i.e. sum of all signals per retention time across all m/z).
getPeaks: signature(object = "xcmsRaw"): get data for peaks in specified m/z and time ranges
getScan: signature(object = "xcmsRaw"): get m/z and intensity values for a single mass scan
getSpec: signature(object = "xcmsRaw"): get average m/z and intensity values for multiple mass scans
image: signature(x = "xcmsRaw"): get data for peaks in specified m/z and time ranges
levelplot: Create an image of the raw (profile) data m/z against retention time, with the intensity color coded.
mslevel: Getter method for the mslevel slot.
plotChrom: signature(object = "xcmsRaw"): plot a chromatogram from profile data
plotRaw: signature(object = "xcmsRaw"): plot locations of raw intensity data points
plotScan: signature(object = "xcmsRaw"): plot a mass spectrum of an individual scan from the raw data
plotSpec: signature(object = "xcmsRaw"): plot a mass spectrum from profile data
plotSurf: signature(object = "xcmsRaw"): experimental method for plotting 3D surface of profile data with rgl.
plotTIC: signature(object = "xcmsRaw"): plot total ion count chromatogram
profinfo: signature(object = "xcmsRaw"): returns a list containing the profile generation method and step (profile m/z step size) and eventual additional parameters to the profile function.
profMedFilt: signature(object = "xcmsRaw"): median filter profile data in time and m/z dimensions
profMethod<-: signature(object = "xcmsRaw"): change the method of generating the profile matrix
profMethod: signature(object = "xcmsRaw"): get the method of generating the profile matrix
profMz: signature(object = "xcmsRaw"): get vector of m/z values for each row of the profile matrix
profRange: signature(object = "xcmsRaw"): interpret flexible ways of specifying subsets of the profile matrix
profStep<-: signature(object = "xcmsRaw"): change the m/z step used for generating the profile matrix
profStep: signature(object = "xcmsRaw"): get the m/z step used for generating the profile matrix
revMz: signature(object = "xcmsRaw"): reverse the order of the data points for each scan
scanrange: Getter method for the scanrange slot. See slot description above for more information.
sortMz: signature(object = "xcmsRaw"): sort the data points by increasing m/z for each scan
stitch: signature(object = "xcmsRaw"): Raw data correction for lock mass calibration gaps.