identify_single_peak: Identify single peak based on database.
In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

identify_single_peak

R Documentation

Identify single peak based on database.

Description

We can use this function to identify single peak, you can just provide m/z or rt, or you can also provide MS2 spectrum for this peak.

Usage

identify_single_peak(
  ms1.mz,
  ms1.rt,
  ms2,
  ms1.match.ppm = 25,
  ms2.match.ppm = 30,
  mz.ppm.thr = 400,
  ms2.match.tol = 0.5,
  fraction.weight = 0.3,
  dp.forward.weight = 0.6,
  dp.reverse.weight = 0.1,
  rt.match.tol = 30,
  polarity = c("positive", "negative"),
  ce = "all",
  column = c("hilic", "rp"),
  ms1.match.weight = 0.25,
  rt.match.weight = 0.25,
  ms2.match.weight = 0.5,
  path = ".",
  total.score.tol = 0.5,
  candidate.num = 3,
  database,
  threads = 3
)

Arguments

`ms1.mz`	m/z value of the peaks
`ms1.rt`	rt value of the peaks
`ms2`	MS2 spectra of the peaks. It must be a two column data frame, the first column is m/z and the second column is the intensity.
`ms1.match.ppm`	Precursor match ppm tolerance.
`ms2.match.ppm`	Fragment ion match ppm tolerance.
`mz.ppm.thr`	Accurate mass tolerance for m/z error calculation.
`ms2.match.tol`	MS2 match (MS2 similarity) tolerance.
`fraction.weight`	The weight for matched fragments.
`dp.forward.weight`	Forward dot product weight.
`dp.reverse.weight`	Reverse dot product weight.
`rt.match.tol`	RT match tolerance.
`polarity`	The polarity of data, "positive"or "negative".
`ce`	Collision energy. Please confirm the CE values in your database. Default is "all".
`column`	"hilic" (HILIC column) or "rp" (reverse phase).
`ms1.match.weight`	The weight of MS1 match for total score calculation.
`rt.match.weight`	The weight of RT match for total score calculation.
`ms2.match.weight`	The weight of MS2 match for total score calculation.
`path`	Work directory.
`total.score.tol`	Total score tolerance. The total score are refering to MS-DIAL.
`candidate.num`	The number of candidate.
`database`	MS2 database name.
`threads`	Number of threads