adductSpecGen {adductomicsR} | R Documentation

## Constructor of AdductSpec object deconvolute spectra MS2 and MS1 levels

### Description

reads mzXML files from a directory extracts metadata info, groups ion signals with `signalGrouping`, filters noise dynamically `dynamicNoiseFilter` and identifies precursor ion charge state, by isotopic pattern.

### Usage

    adductSpecGen(mzXmlDir=NULL, runOrder=NULL, nCores=NULL,
    intStdMass=834.77692,intStdPeakList=c(290.21, 403.30, 516.38,
    587.42,849.40, 884.92, 958.46, 993.97,1050.52, 1107.06, 1209.73,
    1337.79,1465.85),TICfilter=10000, DNF=2, minInt=300,
    minPeaks=5,intStd_MaxMedRtDrift=360, intStd_MaxPpmDev=200,minSpecEx=40,
    outputPlotDir=NULL)

### Arguments

`mzXmlDir` | character a full path to a directory containing either .mzXML or .mzML data
`runOrder` | character a full path to a csv file specifying the runorder for each of the files the first column must contain the precise file name and the second column an integer representing the precise run order.
`nCores` | numeric the number of cores to use for parallel computation. The default is to 1 core
`intStdMass` | numeric vector of the mass of the internal standard. Default is the mass of
`intStdPeakList` | numeric vector of masses for the internal standard peaks
`TICfilter` | numeric minimimum total ion current of an MS/MS scan. Any MS/MS scan below this value will be filtered out (default=0).
`DNF` | dynamic noise filter minimum signal to noise threshold (default = 2), calculated as the ratio between the linear model predicted intensity value and the actual intensity.
`minInt` | numeric minimum intensity value
`minPeaks` | minimum number of signal peaks following dynamic noise filtration (default = 5).
`intStd_MaxMedRtDrift` | numeric the maximum retention time drift window (in seconds) to identify internal standard MS/MS spectrum scans (default = 600).
`intStd_MaxPpmDev` | numeric the maximum mass accuracy window (in ppm). to identify internal standard MS/MS spectrum scans (default = 200 ppm).
`minSpecEx` | numeric the minimum percentage of the total ion current explained by the internal standard fragments (default = 40). Sometime spectra are not identified due to this cutoff being set too high. If unexpected datapoints have been interpolated then reduce this value.
`outputPlotDir` | character string for the output directory for plots, default is working directory.

### Value

AdductSpec object

[Package adductomicsR version 1.0.0 Index]