ms2Annotation: ms2Annotation
In ZhuMSLab/MetDNA: MetDNA

ms2Annotation

R Documentation

ms2Annotation

Description

Annotate peak using MS/MS spectra in in-house database.

Usage

ms2Annotation(ms1.file = "data.csv", instrument = c("AgilentQTOF",
  "SciexTripleTOF", "OtherQTOF", "ThermoOrbitrap"), ms2.file,
  sample.info = "sample.info.csv", mz.tol = 25, rt.tol = 10,
  dp.cutoff = 0.8, polarity = c("positive", "negative"), path = ".",
  output.path = file.path(path, "MS2_match_result"), ms2.type = c("mgf",
  "mzXML", "msp"), column = c("hilic", "rp"), ce = c("30", "10", "20",
  "35,15", "40", "50"), ms2.match.plot = TRUE)

Arguments

`ms1.file`	The name of ms1 peak table. Column 1 is "name", Column 2 is "mz" and column is "rt".
`instrument`	The instrument you used to acquire data. "AgilentQTOF", "SciexTripleTOF", "OtherQTOF" and "ThermoOrbitrap" are supported.
`ms2.file`	The vector of names of ms2 files. MS2 file must be mzXML.
`sample.info`	The name of sample.info.
`mz.tol`	mz tol for ms1 and ms2 data matching.
`rt.tol`	RT tol for ms1 and ms2 data matching.
`dp.cutoff`	The cutoff of dot product. Default is 0.8.
`polarity`	The polarity of mode.
`path`	Directory.
`output.path`	The directory for outputing results.
`ms2.type`	"mgf", "msp" or "mzXML".
`column`	The column.
`ce`	The collision energy.
`ms2.match.plot`	Output MS2 match plot or not.