chromatographicPeakAnalysis {IDSL.IPA}

Chromatography analysis

Description

This function detects individual chromatographic peaks and measures their peak qualification metrics.

Usage

chromatographicPeakAnalysis(spectraScanXIC, aggregatedSpectraList, retentionTime,
LretentionTime, massAccuracy, mzTarget, rtTarget = NULL, scanNumberStart,
scanNumberEnd, smoothingWindow, peakResolvingPower, minNIonPair, minPeakHeight,
minRatioIonPair, maxRPW, minSNRbaseline, maxR13CcumulatedIntensity,
maxPercentageMissingScans, nSpline, exportEICparameters  = NULL)

Arguments

spectraScanXIC

a matrix consists of 5 columns. The column contents are the m/z of 12C isotopologues, intensity of 12C isotopologues, scan number (t), m/z of 13C isotopologues, and intensity of 13C isotopologues, respectively. Redundant scan numbers are not allowed for this module.

aggregatedSpectraList

aggregated spectraList and spectra matrix from the 'IPA_spectraListAggregator' module

retentionTime

a vector of retention times vs. corresponding scan numbers

LretentionTime

length of the retention time vector

massAccuracy

mass error to perform chromatography analysis

mzTarget

m/z value to perform chromatography analysis

rtTarget

retention time value for a targeted peak to calculate the ancillary chromatography parameters. When this parameter set at 0, the ancillary chromatography parameters are calculated for the entire detected peaks.

scanNumberStart

the first scan number.

scanNumberEnd

the last scan number.

smoothingWindow

number of scans for peak smoothing

peakResolvingPower

a value to represent peak resolving power

minNIonPair

minimum number of nIsoPair for an individual peak

minPeakHeight

minimum peak height for an individual peak

minRatioIonPair

minimum ratio of nIsoPair per number of available scans within an individual peak

maxRPW

maximum allowed value of ratio of peak width at half-height to baseline (RPW) for an individual peak

minSNRbaseline

minimum S/N baseline for an individual peak

maxR13CcumulatedIntensity

maximum allowed value of average R13C for an individual peak

maxPercentageMissingScans

maximum allowed value of percentage missing scans on the raw chromatogram for an individual peak.

nSpline

number of points for further smoothing using a cubic spline smoothing method to calculate ancillary chromatographic parameters

exportEICparameters

When ‘NULL', EICs are not plotted. 'exportEICparameters' should contain three variables of 1) an address to save IPA EICs figures, 2) ’HRMS' file name, and 3) a valid string of characters.

Value

a data frame consisting of 24 columns representing chromatography and mass spectrometry parameters. Each row represents an individual separated chromatographic peak.