identify_single_peak: Identify single peak based on database.

View source: R/single_peak_identification.R

identify_single_peakR 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. \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 shenxt1990@163.com

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.