chromatographicPeakAnalysis: Chromatography analysis

In IDSL.IPA: Intrinsic Peak Analysis (IPA) for HRMS Data

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.

IDSL.IPA documentation built on June 7, 2023, 6:01 p.m.