metIdentify: Identify metabolites based on MS/MS database.

View source: R/deprecated_metIdentify.R

metIdentifyR Documentation

Identify metabolites based on MS/MS database.

Description

Identify metabolites based on MS/MS database. \lifecycledeprecated

Usage

metIdentify(
  ms1.data,
  ms2.data = NULL,
  ms1.ms2.match.mz.tol = 25,
  ms1.ms2.match.rt.tol = 10,
  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,
  silence.deprecated = FALSE
)

Arguments

ms1.data

The name of ms1 peak table (csv format). Column 1 is "name", Column 2 is "mz" and column is "rt" (second).

ms2.data

MS2 data, must be mgf, msp or mzXML format. For example, ms2.data = c("test.mgf", "test2.msp").

ms1.ms2.match.mz.tol

MS1 peak and MS2 spectrum matching m/z tolerance. Default is 25 pm.

ms1.ms2.match.rt.tol

MS1 peak and MS2 spectrum matching RT tolerance. Default is 10 s.

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 or MS2 database.

threads

Number of threads

silence.deprecated

Silenc the deprecated information or not.

Value

A metIdentifyClass object.

Author(s)

Xiaotao Shen shenxt1990@163.com

See Also

The example and demo data of this function can be found https://jaspershen.github.io/metID/articles/metID.html

Examples

## Not run: 
##creat a folder nameed as example
path <- file.path(".", "example")
dir.create(path = path, showWarnings = FALSE)

##get MS1 peak table from metID
ms1_peak <- system.file("ms1_peak", package = "metID")
file.copy(from = file.path(ms1_peak, "ms1.peak.table.csv"), 
          to = path, overwrite = TRUE, recursive = TRUE)
ms2_data <- system.file("ms2_data", package = "metID")
file.copy(from = file.path(ms2_data, "QC1_MSMS_NCE25.mgf"), 
          to = path, overwrite = TRUE, recursive = TRUE)
database <- system.file("ms2_database", package = "metID")

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

annotate_result3 <- 
metIdentify(ms1.data = "ms1.peak.table.csv", 
                     ms2.data = c("QC1_MSMS_NCE25.mgf"), 
                     ms2.match.tol = 0.5, 
                     ce = "all",
                     ms1.match.ppm = 15, 
                     rt.match.tol = 30, 
                     polarity = "positive", 
                     column = "rp", 
                     path = path, 
                     candidate.num = 3,
                     database = "msDatabase_rplc0.0.2", 
                     threads = 2)
annotate_result3

## End(Not run)

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