annotate_metabolites: Annotate Metabolites

In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

Annotate Metabolites

Description

This function annotates metabolites in the provided object based on MS1, retention time (RT), and/or MS2 spectra data using a specified database. It allows for customization of matching parameters such as m/z match tolerance, retention time tolerance, and MS2 matching criteria.

Usage

annotate_metabolites(
  object,
  database,
  based_on = c("ms1", "rt", "ms2"),
  polarity = c("positive", "negative"),
  column = c("rp", "hilic"),
  adduct.table = NULL,
  ce = "all",
  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,
  ms1.match.weight = 0.25,
  rt.match.weight = 0.25,
  ms2.match.weight = 0.5,
  total.score.tol = 0.5,
  candidate.num = 3,
  remove_fragment_intensity_cutoff = 0,
  return_format = c("mass_dataset", "data.frame"),
  threads = 3
)

Arguments

object	A 'mass_dataset' object containing MS1, RT, and/or MS2 data.
database	A 'databaseClass' object used for metabolite annotation.
based_on	Character vector. Specifies the matching criteria to be used for annotation. Can include '"ms1"', '"rt"', and/or '"ms2"'. Default is 'c("ms1", "rt", "ms2")'.
polarity	Character. Ionization mode, either '"positive"' or '"negative"'. Default is '"positive"'.
column	Character. The chromatographic column type, either '"hilic"' or '"rp"' (reversed-phase). Default is '"hilic"'.
adduct.table	A data frame specifying the adduct table for metabolite annotation. If 'NULL', a default adduct table is loaded based on polarity and column type.
ce	Character. Collision energy used in MS2. Default is '"all"'.
ms1.match.ppm	Numeric. Mass tolerance in parts per million (ppm) for MS1 peak matching. Default is 25.
ms2.match.ppm	Numeric. Mass tolerance in ppm for MS2 peak matching. Default is 30.
mz.ppm.thr	Numeric. m/z threshold for ppm calculation. Default is 400.
ms2.match.tol	Numeric. Retention time tolerance for MS2 fragment matching. Default is 0.5.
fraction.weight	Numeric. Weight for the fraction of matched fragments in MS2 spectra. Default is 0.3.
dp.forward.weight	Numeric. Weight for the forward dot product score in MS2 matching. Default is 0.6.
dp.reverse.weight	Numeric. Weight for the reverse dot product score in MS2 matching. Default is 0.1.
rt.match.tol	Numeric. Retention time matching tolerance in seconds. Default is 30.
ms1.match.weight	Numeric. Weight for MS1 matching score in the overall annotation score. Default is 0.25.
rt.match.weight	Numeric. Weight for retention time matching score in the overall annotation score. Default is 0.25.
ms2.match.weight	Numeric. Weight for MS2 matching score in the overall annotation score. Default is 0.5.
total.score.tol	Numeric. Tolerance for the total matching score. Default is 0.5.
candidate.num	Numeric. Maximum number of candidate annotations to retain per metabolite. Default is 3.
remove_fragment_intensity_cutoff	Numeric. Cutoff to remove low-intensity MS2 fragments. Default is 0.
return_format	Character. Specifies the format of the output. Can be '"mass_dataset"' or '"data.frame"'. Default is '"mass_dataset"'.
threads	Numeric. Number of threads to use for parallel processing. Default is 3.

Details

This function performs metabolite annotation using a combination of MS1, retention time, and MS2 data (if available) from the provided object. The function allows users to customize the matching process, including setting tolerances for MS1 and MS2 matching, adjusting the weights of different scoring components, and selecting a specific chromatographic column and adduct table.

If 'ms2' is included in the 'based_on' argument, the function extracts both MS1 and MS2 information for annotation. The final annotations are filtered based on the specified score thresholds and only the top 'candidate.num' annotations are retained for each metabolite.

Value

A modified 'mass_dataset' object with annotated metabolites added to the 'annotation_table' slot.

Examples

## Not run: 
# Load a sample dataset and database
my_data <- load_mass_dataset("path/to/data")
my_database <- load_database("path/to/database")

# Annotate metabolites using MS1 and MS2 data
annotated_data <- annotate_metabolites(
  object = my_data,
  database = my_database,
  based_on = c("ms1", "ms2"),
  polarity = "positive",
  column = "rp",
  ms1.match.ppm = 20,
  ms2.match.ppm = 25,
  candidate.num = 5,
  threads = 4
)

## End(Not run)

tidymass/metid documentation built on Oct. 8, 2024, 10:32 p.m.