identify_single_peak: Identify single peak based on database.

In jaspershen/metID: Metabolite identification based on MS1 and MS2 spectra

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. \lifecycleexperimental

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

Value

A metIdentifyClass object.

Author(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
mz <- 115.0508 
rt <- 30
mz = c(87.05525,
88.03929,
91.57985,
91.83949,
91.84950,
97.01802,
98.03480,
98.79539,
115.04163,
115.05016,
115.05354,
115.06940,
129.11253),
intensity = c(280301.375,
             12300.317,
             1339.649,
             1134.635,
             1263.785,
             8685.318,
             2102.683,
             1109.476,
             78187.086,
             153354.766,
             5545.969,
             2884.935,
             1226.609),
stringsAsFactors = FALSE
)

path <- file.path(".", "example")
dir.create(path = path, showWarnings = FALSE)
database <- system.file("ms2_database", package = "metID")

file.copy(from = file.path(database, "msDatabase_rplc0.0.2"), 
         to = path, overwrite = TRUE, recursive = TRUE)

annotation_result <- 
identify_single_peak(ms1.mz = mz, 
                    ms1.rt = rt, 
                    ms2 = ms2, 
                    ms1.match.ppm = 15, 
                    rt.match.tol = 30,
                    ms2.match.tol = 0.5, 
                    database = "msDatabase_rplc0.0.2",
                    path = path)
                    
annotation_result

## End(Not run)

jaspershen/metID documentation built on July 31, 2022, 11:31 p.m.