AssignMSMSParam: AssignMSMSParam
In ZhuMetLab/Sterol4DAnalyzer: Sterol-lipids identifier

View source: R/Function-Params.R

AssignMSMSParam

R Documentation

AssignMSMSParam

Description

Parameters for MSMS assignment

Usage

AssignMSMSParam(
  methodAssign = c("highest"),
  methodRT = c("raw", "corrected"),
  rtTol = 0,
  rtExtend = 90,
  mzTol = 0.01,
  ccsTol = 0.5,
  rtUnitMS1 = c("s", "m"),
  rtUnitMS2 = c("s", "m"),
  isolationWindow = 1,
  thrIsolationIntensity = 150,
  thrIntMS1Predicted = 500,
  snthreshMSMS = 10,
  minfracVote = 0.25,
  outputSpec = FALSE,
  plotMSMSEIC = TRUE,
  typeMSMSEIC = c("pdf", "png", "both"),
  rerun = FALSE
)

Arguments

`methodAssign`	`character` Method for MSMS asignment highest - select the spectrum with highest precursor intensity when fragmentation in all samples consensus - consensus of all found spectra combined" - consensus of spectra selected from each sample with highest precursor intensity when fragmentation
`methodRT`	`character` Raw or corrected RT for MSMS assignment
`rtTol`	`numeric` RT tolerance when matching MSMS spectra and MS1 peaks
`rtExtend`	`numeric` Extended RT tolerance when matching MSMS spectra and MS1 peaks
`mzTol`	`numeric` MZ tolerance when matching MSMS spectra and MS1 peaks mzTol < 1 tolerance in Da mzTol >= 1 tolerance in ppm
`ccsTol`	`numeric` CCS tolerance (in percentage) when matching MSMS spectra and MS1 peaks
`rtUnitMS1`	`character` RT unit for user provided MS1 peak table
`rtUnitMS2`	`character` RT unit for user provided MSMS spectrum files
`isolationWindow`	`numeric` Isolation window when selecting precursor ions for fragmentation
`thrIsolationIntensity`	`numeric` Intensity threshold of the contaminat precorsor ions in isolation window to be extracted
`thrIntMS1Predicted`	`numeric` Intensity threshold of precursor ions for fragmentation to be kept
`snthreshMSMS`	`numeric` S/N threshold for MSMS fragments
`minfracVote`	`numeric` Minimal fraction for presentation of fragment to be kept in consensus spectrum
`outputSpec`	`logical` If output spectra to the spectral MSP file
`plotMSMSEIC`	`logical` If plot EIC with found MSMS specta
`typeMSMSEIC`	`character` Image format (either in PNG or PDF) for plotting
`rerun`	`logical` If rerun all data processing progress
`ppmBinMZ`	`numeric` Minimal mz in ppm for fragment binning
`minBinMZ`	`numeric` Minimal mz in Da for fragment binning
`thrRingMz`	`numeric` MZ tolerance in Da for finding satelite fragments
`thrRingIntRel`	`numeric` Relative intensity tolerance for finding satelite fragments