assessPuritySingle: Assess the purity of a single LC-MS/MS or DI-MS/MS file

In computational-metabolomics/msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Assess the purity of a single LC-MS/MS or DI-MS/MS file

Description

Given a filepath to an mzML file the precursor purity for any MS/MS scans will be outputed into a dataframe

Usage

assessPuritySingle(
  filepth,
  fileid = NA,
  mostIntense = FALSE,
  nearest = TRUE,
  offsets = NA,
  cores = 1,
  plotP = FALSE,
  plotdir = NULL,
  interpol = "linear",
  iwNorm = FALSE,
  iwNormFun = NULL,
  ilim = 0,
  mzRback = "pwiz",
  isotopes = TRUE,
  im = NULL,
  ppmInterp = 7
)

Arguments

filepth	character; mzML file path for MS/MS spectra
fileid	numeric; adds a fileid column (primarily for internal use for msPurity)
mostIntense	boolean; True if the most intense peak is used for calculation. False if the centered peak is used
nearest	boolean; True if the peak selected is as the nearest MS1 scan. If False then the preceding scan is used
offsets	vector; Overide the isolation offsets found in the mzML filee.g. c(0.5, 0.5)
cores	numeric; Number of cores to use
plotP	boolean; If TRUE a plot of the purity is to be saved
plotdir	vector; If plotP is TRUE plots will be saved to this directory
interpol	character; Type of interolation to be performed "linear", "spline" or "none"
iwNorm	boolean; If TRUE then the intensity of the isolation window will be normalised based on the iwNormFun function
iwNormFun	function; A function to normalise the isolation window intensity. The default function is very generalised and just accounts for edge effects
ilim	numeric; All peaks less than this percentage of the target peak will be removed from the purity calculation, default is 5% (0.05)
mzRback	character; Backend to use for mzR parsing
isotopes	boolean; TRUE if isotopes are to be removed
im	matrix; Isotope matrix, default removes C13 isotopes (single, double and triple bonds)
ppmInterp	numeric; Set the ppm tolerance for the precursor ion purity interpolation. i.e. the ppm tolerence between the precursor ion found in the neighbouring scans.

Value

a dataframe of the purity score of the ms/ms spectra

See Also

purityA

Examples

filepth <- system.file("extdata", "lcms", "mzML", "LCMSMS_1.mzML", package="msPurityData")

puritydf <- assessPuritySingle(filepth)

computational-metabolomics/msPurity documentation built on Sept. 8, 2023, 8:04 p.m.