findPeaks.centWaveWithPredictedIsotopeROIs-methods: Feature detection with centWave and additional isotope...

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

Feature detection with centWave and additional isotope features

Description

Peak density and wavelet based feature detection for high resolution LC/MS data in centroid mode with additional peak picking of isotope features on basis of isotope peak predictions

Arguments

object	xcmsSet object
ppm	maxmial tolerated m/z deviation in consecutive scans, in ppm (parts per million)
peakwidth	Chromatographic peak width, given as range (min,max) in seconds
snthresh	signal to noise ratio cutoff, definition see below.
prefilter	prefilter=c(k,I). Prefilter step for the first phase. Mass traces are only retained if they contain at least k peaks with intensity >= I.
mzCenterFun	Function to calculate the m/z center of the feature: wMean intensity weighted mean of the feature m/z values, mean mean of the feature m/z values, apex use m/z value at peak apex, wMeanApex3 intensity weighted mean of the m/z value at peak apex and the m/z value left and right of it, meanApex3 mean of the m/z value at peak apex and the m/z value left and right of it.
integrate	Integration method. If =1 peak limits are found through descent on the mexican hat filtered data, if =2 the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.
mzdiff	minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap
fitgauss	logical, if TRUE a Gaussian is fitted to each peak
scanrange	scan range to process
noise	optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity < noise are omitted from ROI detection
sleep	number of seconds to pause between plotting peak finding cycles
verbose.columns	logical, if TRUE additional peak meta data columns are returned
ROI.list	A optional list of ROIs that represents detected mass traces (ROIs). If this list is empty (default) then centWave detects the mass trace ROIs, otherwise this step is skipped and the supplied ROIs are used in the peak detection phase. Each ROI object in the list has the following slots: scmin start scan index, scmax end scan index, mzmin minimum m/z, mzmax maximum m/z, length number of scans, intensity summed intensity.
firstBaselineCheck	logical, if TRUE continuous data within ROI is checked to be above 1st baseline
roiScales	numeric, optional vector of scales for each ROI in ROI.list to be used for the centWave-wavelets
snthreshIsoROIs	signal to noise ratio cutoff for predicted isotope ROIs, definition see below.
maxcharge	max. number of the isotope charge.
maxiso	max. number of the isotope peaks to predict for each detected feature.
mzIntervalExtension	logical, if TRUE predicted isotope ROIs (regions of interest) are extended in the m/z dimension to increase the detection of low intensity and hence noisy peaks.

Details

This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode. The centWave algorithm is applied in two peak picking steps as follows. In the first peak picking step ROIs (regions of interest, characterised as regions with less than ppm m/z deviation in consecutive scans) in the LC/MS map are located and further analysed using continuous wavelet transform (CWT) for the localization of chromatographic peaks on different scales. In the second peak picking step isotope ROIs in the LC/MS map are predicted further analysed using continuous wavelet transform (CWT) for the localization of chromatographic peaks on different scales. The peak lists resulting from both peak picking steps are merged and redundant peaks are removed.

Value

A matrix with columns:

mz	weighted (by intensity) mean of peak m/z across scans
mzmin	m/z peak minimum
mzmax	m/z peak maximum
rt	retention time of peak midpoint
rtmin	leading edge of peak retention time
rtmax	trailing edge of peak retention time
into	integrated peak intensity
intb	baseline corrected integrated peak intensity
maxo	maximum peak intensity
sn	Signal/Noise ratio, defined as (maxo - baseline)/sd, where maxo is the maximum peak intensity, baseline the estimated baseline value and sd the standard deviation of local chromatographic noise.
egauss	RMSE of Gaussian fit
	if verbose.columns is TRUE additionally :
mu	Gaussian parameter mu
sigma	Gaussian parameter sigma
h	Gaussian parameter h
f	Region number of m/z ROI where the peak was localised
dppm	m/z deviation of mass trace across scans in ppm
scale	Scale on which the peak was localised
scpos	Peak position found by wavelet analysis
scmin	Left peak limit found by wavelet analysis (scan number)
scmax	Right peak limit found by wavelet analysis (scan number)

Methods

object = "xcmsRaw"

findPeaks.centWaveWithPredictedIsotopeROIs(object, ppm=25, peakwidth=c(20,50), snthresh=10, prefilter=c(3,100), mzCenterFun="wMean", integrate=1, mzdiff=-0.001, fitgauss=FALSE, scanrange= numeric(), noise=0, sleep=0, verbose.columns=FALSE, ROI.list=list(), firstBaselineCheck=TRUE, roiScales=NULL, snthreshIsoROIs=6.25, maxcharge=3, maxiso=5, mzIntervalExtension=TRUE)

Author(s)

Ralf Tautenhahn

References

Ralf Tautenhahn, Christoph B\"ottcher, and Steffen Neumann "Highly sensitive feature detection for high resolution LC/MS" BMC Bioinformatics 2008, 9:504\ Hendrik Treutler and Steffen Neumann. "Prediction, detection, and validation of isotope clusters in mass spectrometry data" Submitted to Metabolites 2016, Special Issue "Bioinformatics and Data Analysis"

See Also

do_findChromPeaks_centWaveWithPredIsoROIs for the corresponding core API function. findPeaks.addPredictedIsotopeFeatures findPeaks.centWave findPeaks-methods xcmsRaw-class

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.