metIdentify: Identify metabolites based on MS/MS database.

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

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 [e-mail]

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.