identify_peak: Identify metabolites based on MS1 or MS/MS database

In Coayala/MetaboTandem: Pipeline for the analysis of LC-MS/MS data

Identify metabolites based on MS1 or MS/MS database

Description

Identify metabolites based on MS1 or MS/MS database.

Usage

identify_peak(
  idx,
  ms1.info,
  ms2.info,
  spectra.info,
  spectra.data,
  ppm.ms1match = 25,
  ppm.ms2match = 30,
  mz.ppm.thr = 400,
  ms2.match.tol = 0.5,
  rt.match.tol = 30,
  ms1.match.weight = 0.25,
  rt.match.weight = 0.25,
  ms2.match.weight = 0.5,
  total.score.tol = 0.5,
  adduct.table,
  candidate.num = 3,
  fraction.weight = 0.3,
  dp.forward.weight = 0.6,
  dp.reverse.weight = 0.1,
  remove_fragment_intensity_cutoff = 0,
  ...
)

Arguments

idx	idx
ms1.info	ms1.info
ms2.info	ms2.info
spectra.info	spectra.info
spectra.data	spectra.data
ppm.ms1match	ppm.ms1match
ppm.ms2match	ppm.ms2match
mz.ppm.thr	Accurate mass tolerance for m/z error calculation.
ms2.match.tol	MS2 match (MS2 similarity) tolerance.
rt.match.tol	The weight for matched fragments.
ms1.match.weight	Forward dot product weight.
rt.match.weight	Reverse dot product weight.
ms2.match.weight	RT match tolerance.
total.score.tol	The polarity of data, "positive"or "negative".
adduct.table	Collision energy. Please confirm the CE values in your database. Default is "all".
candidate.num	"hilic" (HILIC column) or "rp" (reverse phase).
fraction.weight	The weight of MS1 match for total score calculation.
dp.forward.weight	The weight of RT match for total score calculation.
dp.reverse.weight	The weight of MS2 match for total score calculation.
remove_fragment_intensity_cutoff	remove_fragment_intensity_cutoff
...	other parameters

Value

A metIdentifyClass object.

Author(s)

Xiaotao Shen [e-mail]

Coayala/MetaboTandem documentation built on April 7, 2024, 3:39 a.m.