Version checked for this guide: 1.3.2 · 2026-09-23
metid matches precursor masses, compatible RT and available MS2 against a databaseClass. Import or construct the reference database and attach experimental MS2 to your mass_dataset first. Check ion polarity, chromatography and adduct settings.
The current API includes annotate_metabolites_mass_dataset() alongside established metIdentify* and mzIdentify* interfaces. Do not mix argument names from different interfaces. The example explicitly disables RT evidence for a reference whose chromatography is not comparable. Review tolerances against your instrument; these values are illustrative.
Inspect all candidate evidence, not just a top score. An MS1 candidate is not a confirmed structure. An in-house database can support stronger identification when standards and measurements meet the actual evidence criteria; the database’s name alone does not establish confidence. Retain ambiguous candidates and record any filtering or adduct de-duplication. Origin annotations report database associations, not direct evidence of synthesis in your sample.
Functional scope
Database construction and validation; MS1/MS2 annotation; single-peak queries; matching scores and mirror spectra; confidence/candidate/adduct filtering; origin summaries.
Example
# Requires an MS2-associated object and a compatible databaseClass.
# database <- readRDS("reference_database.rds")
# annotated <- metid::annotate_metabolites_mass_dataset(
# object = object, database = database,
# polarity = "positive", column = "rp",
# ms1.match.ppm = 15, ms2.match.ppm = 30,
# rt.match.tol = NA, rt.match.weight = 0,
# candidate.num = 3, threads = 2
# )
help("annotate_metabolites_mass_dataset", package = "metid")
Find a function
The checked source exports the following APIs, including compatibility interfaces and utilities. Consult the installed version with help("function_name", package = "metid") for argument details.
Show exported functions
analyze_metabolite_origins, annotate_metabolites, annotate_metabolites_mass_dataset, annotate_peaks_mz_rt_ms2, annotate_single_peak_mass_dataset, calculate_confidence_level, calculate_dotproduct, calculate_ms2_matching_score, calculate_mz_match_score, calculate_rt_match_score, calculate_total_score, check_adduct_table, check_database, check_mass_dataset, check_ms1_ms2_info, check_object4metablite_origin, check_parameters4annotate_metabolites, check_parameters4calculate_total_score, construct_database, construct_massbank_database, construct_mona_database, correct_database_rt, extract_database_name, extract_ms1_database, extract_ms1_info, extract_ms2_database, extract_ms2_info, filter, filter_adducts, filter_identification, getIdentificationTable2, getMS2spectrum, get_iden_info, get_identification_table, get_identification_table_all, get_ms2_spectrum, get_ms2_spectrum_from_object, get_parameters, get_parameters_metid, identify_metabolite_all, identify_metabolites, identify_metabolites_params, identify_ms2_only, identify_peak, identify_single_peak, load_adduct_table, match_ms2_fragments, match_ms2_temp, metIdentification, metIdentify, metIdentify_mass_dataset, metabolite_origin_network, metabolite_origin_upsetplot, metid, metid_conflicts, metid_logo, metid_packages, ms2_plot_mass_dataset, ms2plot, mzIdentify, mzIdentifyParam, mzIdentify_mass_dataset, plot_ms2_matching, readMGF, readMSP, readMSP_MoNA, readMZXML, read_mgf_experiment, read_mgf_gnps, read_mgf_mona, read_msp, read_msp_database, read_msp_gnps, read_msp_mona, remove_impossible_annotations, remove_impossible_annotations_fix, remove_noise, source_metabolite_network, source_network, specific_source_network, summary_annotation_table, trans_to_new_style, which_has_identification, write_mgf_gnps, write_mgf_massbank, write_mgf_mona, write_msp, write_msp_gnps, write_msp_massbank, write_msp_mona
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