文档核对版本: 1.3.2 · 2026-09-23
metid 将前体质量、条件相容的 RT 及可用 MS2 与 databaseClass 匹配。先导入或构建参考数据库，再给 mass_dataset 关联实验 MS2，核对离子模式、色谱和加合物。
当前 API 包含 annotate_metabolites_mass_dataset()，也保留 metIdentify*、mzIdentify* 等接口，不能混用参数名。下例针对色谱不可比的参考库明确关闭 RT 证据；质量容差需依据自己的仪器设置，示例值只用于说明。
审查完整候选证据，不只看最高分。MS1 候选不是结构确认；自建库也需要标准品和实际测量满足证据要求，不能仅按库名判断置信度。保留歧义，记录候选筛选和加合物去重规则。来源注释是数据库关联，不是样品中实际合成来源的直接证明。
功能范围
数据库构建校验、MS1/MS2 注释、单峰查询、匹配分数和镜像谱、置信度/候选/加合物筛选及来源汇总。
使用示例
# 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")
函数查询
下面列出已核对源码中导出的 API，包括兼容接口与辅助函数。具体参数以安装版本的 R 帮助为准；例如运行 help("函数名", package = "metid")。
展开导出函数列表
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