mzIdentify_mass_dataset: Metabolite Identification in a mass_dataset Object Using MS1...

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

Metabolite Identification in a mass_dataset Object Using MS1 Data

Description

This function identifies potential metabolites in a 'mass_dataset' object by matching MS1 data (m/z) with a reference spectral database. Optionally, retention time (RT) can also be used for more accurate matching.

Usage

mzIdentify_mass_dataset(
  object,
  ms1.match.ppm = 25,
  rt.match.tol = 30,
  polarity = c("positive", "negative"),
  column = c("hilic", "rp"),
  candidate.num = 3,
  database,
  threads = 3
)

Arguments

object	A 'mass_dataset' object that contains MS1 data.
ms1.match.ppm	A numeric value specifying the mass accuracy threshold for MS1 matching in parts per million (ppm). Defaults to '25'.
rt.match.tol	A numeric value specifying the retention time matching tolerance in seconds. Defaults to '30'. If set to a large value (e.g., greater than '10000'), RT matching will not be performed.
polarity	A character string specifying the ionization mode. It can be either '"positive"' or '"negative"'. Defaults to '"positive"'.
column	A character string specifying the chromatographic column type, either '"hilic"' (hydrophilic interaction) or '"rp"' (reverse phase). Defaults to '"hilic"'.
candidate.num	A numeric value specifying the number of top candidates to retain per feature. Defaults to '3'.
database	A 'databaseClass' object containing the reference spectral database for annotation.
threads	An integer specifying the number of threads to use for parallel processing. Defaults to '3'.

Details

This function performs MS1-based matching between the experimental data in the 'mass_dataset' object and a reference spectral database. The matching process is based on mass-to-charge ratio (m/z) and optionally retention time (RT). The function supports both positive and negative ionization modes and can work with either HILIC or reverse-phase columns.

Value

A data frame containing the metabolite identification results, including m/z error, RT error, matching scores, and information about the identified compounds.

Author(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
# Perform MS1-based metabolite identification in a mass_dataset object
identification_result <- mzIdentify_mass_dataset(
  object = mass_object,
  ms1.match.ppm = 20,
  rt.match.tol = 30,
  polarity = "positive",
  database = reference_database,
  threads = 4
)

## End(Not run)

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