Extracting direct infusion spectra using MassSpecWavelet

May 29, 2012, 02:40:47 PM

Hi,

I would like to extract m/z from a sample set of direct infusion MS data. To achieve that I am using MassSpecWavelet function. There is few parameters so it is easy to use but I don't know how to optimize "scales of CWT" (see below).
Is someone has ever worked with this function and can help me to choose the best value for the scale.
Or if you have any suggestion on how to extract direct infusion MS data...
Thanks

Aurelie
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findPeaks.MSW-methods Feature detection for single-spectrum non-chromatography MS data
Description: Processing Mass Spectrometry direct-injection spectrum by using wavelet based algorithm.
Arguments:
object = xcmsSet object
snthresh = signal to noise ratio cutoff
scales = scales of CWT
nearbyPeak = Determine whether to include the nearby small peaks of major peaks. TRUE by default
sleep = number of seconds to pause between plotting peak finding cycles
verbose.columns = additional peak meta data columns are returned
Details:
This is a wrapper around the peak picker in the bioconductor package MassSpecWavelet calling ’cwt’, get.localMaximum.cwt’, ’get.ridge’, ’identify.majorPeaks’ and tuneIn.peakInfo.findPeaks.centWave-methods 15

Value:
A matrix with columns:
mz m/z value of the peak at the centroid position
mzmin m/z value at the start-point of the peak
mzmax m/z value at the end-point of the peak
rt always -1
rtmin always -1
rtmax always -1
into integrated area of original (raw) peak
maxo intensity of original (raw) peak at the centroid position
intf always NA
maxf maximum MSW-filter response of the peak
sn Signal/Noise ratio
Methods
object = "xcmsRaw" findPeaks.MSW(object, snthresh=3, scales=seq(1,22,3), nearbyPeak=TRUE,