3 Performing Taxonomically Informed Metabolite Annotation

Author

Adriano Rutz

Published

October 27, 2025

This vignette describes how Taxonomically Informed Metabolite Annotation is performed. If you followed all previous steps successfully, this should be a piece of cake, you deserve it!

tima::tima_full()
#> + par_def_ann_spe dispatched
#> ✔ par_def_ann_spe completed [28ms, 2.14 kB]
#> + par_def_wei_ann dispatched
#> ✔ par_def_wei_ann completed [0ms, 5.05 kB]
#> + par_def_pre_ann_gnp dispatched
#> ✔ par_def_pre_ann_gnp completed [1ms, 1.42 kB]
#> + par_def_pre_lib_sop_mer dispatched
#> ✔ par_def_pre_lib_sop_mer completed [0ms, 3.40 kB]
#> + yaml_paths dispatched
#> ✔ yaml_paths completed [0ms, 11.52 kB]
#> + par_def_pre_lib_sop_lot dispatched
#> ✔ par_def_pre_lib_sop_lot completed [1ms, 494 B]
#> + par_def_ann_mas dispatched
#> ✔ par_def_ann_mas completed [1ms, 6.09 kB]
#> + par_def_pre_lib_sop_hmd dispatched
#> ✔ par_def_pre_lib_sop_hmd completed [1ms, 492 B]
#> + par_def_fil_ann dispatched
#> ✔ par_def_fil_ann completed [1ms, 1.34 kB]
#> + par_def_pre_lib_sop_clo dispatched
#> ✔ par_def_pre_lib_sop_clo completed [0ms, 523 B]
#> + par_def_pre_lib_spe dispatched
#> ✔ par_def_pre_lib_spe completed [1ms, 1.57 kB]
#> + par_def_pre_fea_com dispatched
#> ✔ par_def_pre_fea_com completed [1ms, 358 B]
#> + par_def_cre_com dispatched
#> ✔ par_def_cre_com completed [1ms, 375 B]
#> + par_def_cre_edg_spe dispatched
#> ✔ par_def_cre_edg_spe completed [1ms, 1.42 kB]
#> + par_def_pre_fea_edg dispatched
#> ✔ par_def_pre_fea_edg completed [1ms, 706 B]
#> + par_def_pre_fea_tab dispatched
#> ✔ par_def_pre_fea_tab completed [1ms, 860 B]
#> + par_def_pre_lib_rt dispatched
#> ✔ par_def_pre_lib_rt completed [0ms, 2.05 kB]
#> + par_def_pre_ann_spe dispatched
#> ✔ par_def_pre_ann_spe completed [1ms, 1.46 kB]
#> + par_def_pre_ann_sir dispatched
#> ✔ par_def_pre_ann_sir completed [1ms, 1.93 kB]
#> + par_def_pre_tax dispatched
#> ✔ par_def_pre_tax completed [1ms, 1.51 kB]
#> + par_def_pre_lib_sop_ecm dispatched
#> ✔ par_def_pre_lib_sop_ecm completed [0ms, 492 B]
#> + paths dispatched
#> ✔ paths completed [1ms, 2.52 kB]
#> + lib_spe_exp_gnp_pre_sop dispatched
#> ::notice title=INFO::Directory data/interim/libraries/sop created.
#> ✔ lib_spe_exp_gnp_pre_sop completed [287ms, 1.42 MB]
#> + lib_spe_exp_mb_pre_sop dispatched
#> ✔ lib_spe_exp_mb_pre_sop completed [78ms, 480.97 kB]
#> + lib_spe_exp_mer_pre_sop dispatched
#> ✔ lib_spe_exp_mer_pre_sop completed [185ms, 1.19 MB]
#> + lib_spe_is_wik_pre_sop dispatched
#> ✔ lib_spe_is_wik_pre_sop completed [208ms, 37.90 MB]
#> + lib_spe_exp_mb_pre_pos dispatched
#> ::notice title=INFO::Directory data/interim/libraries/spectra/exp created.
#> ✔ lib_spe_exp_mb_pre_pos completed [165ms, 19.41 MB]
#> + par_pre_par dispatched
#> ✔ par_pre_par completed [0ms, 1.38 kB]
#> + lib_spe_exp_mer_pre_neg dispatched
#> ✔ lib_spe_exp_mer_pre_neg completed [200ms, 31.54 MB]
#> + lib_spe_is_wik_pre_neg dispatched
#> ::notice title=INFO::Directory data/interim/libraries/spectra/is created.
#> ✔ lib_spe_is_wik_pre_neg completed [1.8s, 687.33 MB]
#> + par_pre_par2 dispatched
#> ✔ par_pre_par2 completed [0ms, 21.17 kB]
#> + lib_spe_is_wik_pre_pos dispatched
#> Downloading  42% ■■■■■■■■■■■■■■                    1s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> ✔ lib_spe_is_wik_pre_pos completed [2.8s, 863.95 MB]
#> + lib_sop_lot dispatched
#> ::notice title=INFO::Downloading 230106_frozen_metadata.csv.gz from https://doi.org/10.5281/zenodo.5794106 (The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata); unique identifier: https://doi.org/10.5281/zenodo.7534071)
#> ::notice title=INFO::Directory data/source/libraries/sop created.
#> ✔ lib_sop_lot completed [33.3s, 92.98 MB]
#> + lib_sop_hmd dispatched
#> ::notice title=INFO::Directory data/source/libraries/sop/hmdb created.
#> Downloading   1% ■                                 1m
#> Downloading  52% ■■■■■■■■■■■■■■■■■                 3s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> ✔ lib_sop_hmd completed [5s, 96.48 MB]
#> + lib_spe_exp_gnp_pre_neg dispatched
#> Downloading  49% ■■■■■■■■■■■■■■■■                  1s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> ✔ lib_spe_exp_gnp_pre_neg completed [2.4s, 154.12 MB]
#> + lib_spe_exp_mer_pre_pos dispatched
#> ✔ lib_spe_exp_mer_pre_pos completed [1.5s, 84.94 MB]
#> + lib_sop_ecm dispatched
#> ✔ lib_sop_ecm completed [959ms, 1.33 MB]
#> + lib_spe_exp_mb_pre_neg dispatched
#> ✔ lib_spe_exp_mb_pre_neg completed [541ms, 7.06 MB]
#> + lib_spe_exp_gnp_pre_pos dispatched
#> Downloading  16% ■■■■■■                            5s
#> Downloading  56% ■■■■■■■■■■■■■■■■■■                3s
#> Downloading  85% ■■■■■■■■■■■■■■■■■■■■■■■■■■        1s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> ✔ lib_spe_exp_gnp_pre_pos completed [9s, 481.27 MB]
#> + par_fin_par dispatched
#> ✔ par_fin_par completed [1ms, 307 B]
#> + par_fin_par2 dispatched
#> ✔ par_fin_par2 completed [2ms, 2.96 kB]
#> + par_usr_pre_lib_sop_mer dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ::notice title=INFO::Directory params/user created.
#> ✔ par_usr_pre_lib_sop_mer completed [1.5s, 1.55 kB]
#> + par_usr_pre_lib_sop_lot dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_lib_sop_lot completed [1.3s, 174 B]
#> + par_usr_pre_tax dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_tax completed [1.3s, 438 B]
#> + par_usr_pre_ann_gnp dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_ann_gnp completed [1.3s, 708 B]
#> + par_usr_pre_lib_sop_hmd dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_lib_sop_hmd completed [1.3s, 178 B]
#> + par_usr_cre_com dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_cre_com completed [1.3s, 200 B]
#> + par_usr_pre_lib_sop_clo dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_lib_sop_clo completed [1.5s, 205 B]
#> + par_usr_cre_edg_spe dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_cre_edg_spe completed [1.3s, 452 B]
#> + par_usr_pre_fea_com dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_fea_com completed [1.3s, 200 B]
#> + par_usr_pre_fea_edg dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_fea_edg completed [1.3s, 328 B]
#> + par_usr_pre_lib_sop_ecm dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_lib_sop_ecm completed [1.3s, 176 B]
#> + par_usr_fil_ann dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_fil_ann completed [1.3s, 668 B]
#> + par_usr_pre_fea_tab dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_fea_tab completed [1.3s, 274 B]
#> + par_usr_pre_lib_rt dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_lib_rt completed [1.3s, 440 B]
#> + par_usr_ann_spe dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_ann_spe completed [1.3s, 1.03 kB]
#> + par_usr_pre_ann_spe dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_ann_spe completed [1.3s, 731 B]
#> + par_usr_pre_lib_spe dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_lib_spe completed [1.3s, 298 B]
#> + par_usr_pre_ann_sir dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_pre_ann_sir completed [1.3s, 900 B]
#> + par_usr_ann_mas dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_ann_mas completed [1.3s, 2.68 kB]
#> + par_usr_wei_ann dispatched
#> ::debug::Loading default params
#> ::debug::All params
#> ::debug::Small params
#> ::debug::Advanced params
#> ::debug::Changing params
#> ::debug::Changing filenames
#> ::debug::Exporting params
#> ✔ par_usr_wei_ann completed [1.3s, 1.76 kB]
#> + par_pre_lib_sop_mer dispatched
#> ✔ par_pre_lib_sop_mer completed [1ms, 558 B]
#> + par_pre_lib_sop_lot dispatched
#> ✔ par_pre_lib_sop_lot completed [0ms, 186 B]
#> + par_pre_tax dispatched
#> ✔ par_pre_tax completed [0ms, 327 B]
#> + par_pre_ann_gnp dispatched
#> ✔ par_pre_ann_gnp completed [1ms, 336 B]
#> + par_pre_lib_sop_hmd dispatched
#> ✔ par_pre_lib_sop_hmd completed [1ms, 191 B]
#> + par_cre_com dispatched
#> ✔ par_cre_com completed [0ms, 191 B]
#> + par_pre_lib_sop_clo dispatched
#> ✔ par_pre_lib_sop_clo completed [0ms, 213 B]
#> + par_cre_edg_spe dispatched
#> ✔ par_cre_edg_spe completed [1ms, 389 B]
#> + par_pre_fea_com dispatched
#> ✔ par_pre_fea_com completed [0ms, 184 B]
#> + par_pre_fea_edg dispatched
#> ✔ par_pre_fea_edg completed [1ms, 244 B]
#> + par_pre_lib_sop_ecm dispatched
#> ✔ par_pre_lib_sop_ecm completed [0ms, 191 B]
#> + par_fil_ann dispatched
#> ✔ par_fil_ann completed [1ms, 347 B]
#> + par_pre_fea_tab dispatched
#> ✔ par_pre_fea_tab completed [1ms, 278 B]
#> + par_pre_lib_rt dispatched
#> ✔ par_pre_lib_rt completed [1ms, 329 B]
#> + par_ann_spe dispatched
#> ✔ par_ann_spe completed [1ms, 497 B]
#> + par_pre_ann_spe dispatched
#> ✔ par_pre_ann_spe completed [1ms, 334 B]
#> + par_pre_lib_spe dispatched
#> ✔ par_pre_lib_spe completed [0ms, 305 B]
#> + par_pre_ann_sir dispatched
#> ✔ par_pre_ann_sir completed [1ms, 405 B]
#> + par_ann_mas dispatched
#> ✔ par_ann_mas completed [1ms, 1.13 kB]
#> + par_wei_ann dispatched
#> ✔ par_wei_ann completed [1ms, 932 B]
#> + lib_sop_mer_str_pro dispatched
#> ::notice title=INFO::Directory data/interim/libraries/sop/merged/structures created.
#> ✔ lib_sop_mer_str_pro completed [383ms, 90.51 MB]
#> + lib_sop_lot_pre dispatched
#> ::debug::Loading and preparing LOTUS
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/lotus_prepared.tsv.gz
#> ✔ lib_sop_lot_pre completed [13.9s, 46.52 MB]
#> + lib_sop_hmd_pre dispatched
#> ::debug::Unzipping HMDB
#> ::debug::Loading HMDB
#> ::debug::Formatting HMDB
#> ::debug::Deleting unzipped file
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/hmdb_prepared.tsv.gz
#> ✔ lib_sop_hmd_pre completed [44.6s, 8.06 MB]
#> + lib_sop_clo_pre dispatched
#> ::warning title=WARN::Sorry, you do not have access to the closed resource,
#> returning an empty file instead
#> ::notice title=INFO::Directory data/interim/params created.
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/closed_prepared.tsv.gz
#> ✔ lib_sop_clo_pre completed [21ms, 273 B]
#> + lib_sop_ecm_pre dispatched
#> ::debug::Loading ECMDB resources
#> ::debug::Formatting ECMDB
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/ecmdb_prepared.tsv.gz
#> ✔ lib_sop_ecm_pre completed [641ms, 177.47 kB]
#> + par_pre_fea_tab_fil_fea_raw dispatched
#> ✔ par_pre_fea_tab_fil_fea_raw completed [1ms, 451.55 kB]
#> + lib_rt dispatched
#> ::warning title=WARN::No retention time library found, returning empty sop table.
#> ::warning title=WARN::No retention time library found, returning empty retention time table.
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::Directory data/interim/libraries/rt created.
#> ::notice title=INFO::... path to export is data/interim/libraries/rt/prepared.tsv.gz
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/rt_prepared.tsv.gz
#> ✔ lib_rt completed [52ms, 182 B]
#> + par_ann_spe_fil_spe_raw dispatched
#> ✔ par_ann_spe_fil_spe_raw completed [0ms, 7.77 MB]
#> + lib_spe_exp_int_pre dispatched
#> ::warning title=WARN::Your input file does not exist, returning empty lib instead.
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/internal_prepared.tsv.gz
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ✔ lib_spe_exp_int_pre completed [1.3s, 155 B]
#> + input_features dispatched
#> ✔ input_features completed [1ms, 451.55 kB]
#> + lib_rt_sop dispatched
#> ✔ lib_rt_sop completed [0ms, 96 B]
#> + lib_rt_rts dispatched
#> ✔ lib_rt_rts completed [1ms, 86 B]
#> + input_spectra dispatched
#> ✔ input_spectra completed [0ms, 7.77 MB]
#> + lib_spe_exp_int_pre_sop dispatched
#> ✔ lib_spe_exp_int_pre_sop completed [0ms, 106 B]
#> + lib_spe_exp_int_pre_pos dispatched
#> ✔ lib_spe_exp_int_pre_pos completed [0ms, 601 B]
#> + lib_spe_exp_int_pre_neg dispatched
#> ✔ lib_spe_exp_int_pre_neg completed [0ms, 601 B]
#> + fea_pre dispatched
#> ::debug::Preparing features table
#> ::debug::Formatting feature table
#> ::debug::... requires 'Peak area' or ':area' in columns (mzmine format)
#> ::debug::... or 'quant_' in columns (SLAW format)
#> ::debug::... or 'Peak height' in columns (SIRIUS format)
#> ::debug::Filtering top intensities per feature
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::Directory data/interim/features created.
#> ::notice title=INFO::... path to export is data/interim/features/example_features.tsv.gz
#> ✔ fea_pre completed [151ms, 95.63 kB]
#> + fea_edg_spe dispatched
#> ::notice title=INFO::Read 10000 spectra...
#> ::debug::Harmonizing names
#> ::debug::Filtering MS2 only
#> ::debug::Combining spectra in case
#> ::debug::Applying sanitization of the spectra
#> ::debug::Filtering empty spectra
#> ::notice title=INFO::Considering 3840 spectra
#> ::debug::Performing spectral comparison
#> ::debug::As we do not limit the precursors delta,
#> expect a (relatively) long processing time.
#> ::notice title=INFO::===========================================================
#> ::notice title=INFO::= Take yourself a break, you deserve it.                  =
#> ::notice title=INFO::===========================================================
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#>  ■■■■■■■■■■■■■■■■■                 54% |  ETA:  2m
#>  ■■■■■■■■■■■■■■■■■■                56% |  ETA:  2m
#>  ■■■■■■■■■■■■■■■■■■                58% |  ETA:  2m
#>  ■■■■■■■■■■■■■■■■■■■               60% |  ETA:  2m
#>  ■■■■■■■■■■■■■■■■■■■■              62% |  ETA:  2m
#>  ■■■■■■■■■■■■■■■■■■■■              64% |  ETA:  2m
#>  ■■■■■■■■■■■■■■■■■■■■■             67% |  ETA:  1m
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#>  ■■■■■■■■■■■■■■■■■■■■■■■■■         79% |  ETA: 47s
#>  ■■■■■■■■■■■■■■■■■■■■■■■■■■        84% |  ETA: 36s
#>  ■■■■■■■■■■■■■■■■■■■■■■■■■■■■      89% |  ETA: 22s
#> ::debug::Calculating features' entropy
#> ::debug::Counting features' number of peaks
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/features/example_edgesSpectra.tsv
#> ✔ fea_edg_spe completed [3m 22.6s, 533.82 kB]
#> + lib_sop_mer dispatched
#> ::debug::Loading and concatenating prepared libraries
#> ::debug::Splitting the concatenated library into smaller standardized pieces
#> ::debug::Sanitizing structures
#> ::debug::Processing SMILES
#> ::notice title=INFO::Passing 61 SMILES to RDKit
#> [10:13:37] Explicit valence for atom # 1 N, 3, is greater than permitted
#> [10:13:37] ERROR: Could not sanitize molecule on line 1
#> [10:13:37] ERROR: Explicit valence for atom # 1 N, 3, is greater than permitted
#> [10:13:37] Explicit valence for atom # 0 P, 11, is greater than permitted
#> [10:13:37] ERROR: Could not sanitize molecule on line 2
#> [10:13:37] ERROR: Explicit valence for atom # 0 P, 11, is greater than permitted
#> [10:13:37] Explicit valence for atom # 21 N, 4, is greater than permitted
#> [10:13:37] ERROR: Could not sanitize molecule on line 3
#> [10:13:37] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
#> [10:13:37] Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [10:13:37] ERROR: Could not sanitize molecule on line 4
#> [10:13:37] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [10:13:37] Explicit valence for atom # 6 C, 5, is greater than permitted
#> [10:13:37] ERROR: Could not sanitize molecule on line 5
#> [10:13:37] ERROR: Explicit valence for atom # 6 C, 5, is greater than permitted
#> [10:13:37] Explicit valence for atom # 18 S, 7, is greater than permitted
#> [10:13:37] ERROR: Could not sanitize molecule on line 6
#> [10:13:37] ERROR: Explicit valence for atom # 18 S, 7, is greater than permitted
#> [10:13:37] SMILES Parse Error: syntax error while parsing: OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1
#> [10:13:37] SMILES Parse Error: check for mistakes around position 76:
#> [10:13:37] C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C
#> [10:13:37] ~~~~~~~~~~~~~~~~~~~~^
#> [10:13:37] SMILES Parse Error: extra open parentheses while parsing: OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1
#> [10:13:37] SMILES Parse Error: check for mistakes around position 32:
#> [10:13:37] C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2
#> [10:13:37] ~~~~~~~~~~~~~~~~~~~~^
#> [10:13:37] SMILES Parse Error: extra open parentheses while parsing: OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1
#> [10:13:37] SMILES Parse Error: check for mistakes around position 49:
#> [10:13:37] )\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2
#> [10:13:37] ~~~~~~~~~~~~~~~~~~~~^
#> [10:13:37] SMILES Parse Error: extra open parentheses while parsing: OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1
#> [10:13:37] SMILES Parse Error: check for mistakes around position 66:
#> [10:13:37] )=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(
#> [10:13:37] ~~~~~~~~~~~~~~~~~~~~^
#> [10:13:37] SMILES Parse Error: Failed parsing SMILES 'OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1' for input: 'OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1'
#> [10:13:37] ERROR: Smiles parse error on line 7
#> [10:13:37] ERROR: Cannot create molecule from : 'OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1'
#> ::notice title=INFO::Led to 877903 referenced structure-organism pairs
#> ::notice title=INFO::Corresponding to 393389 unique stereoisomers (excluding structures without stereochemistry)...
#> ::notice title=INFO::... and 1007790 unique structures without stereochemistry...
#> ::notice title=INFO::... or 1184311 unique constitutional isomers (ignoring stereochemistry)
#> ::notice title=INFO::... among 36800 unique organisms
#> ::debug::Keeping keys
#> ::debug::Keeping organisms
#> ::debug::Completing organisms taxonomy
#> ::debug::Testing if Open Tree of Life API is up
#> ::debug::Success! Submitting request
#> ::debug::Request finished!
#> ::debug::Getting taxonomy
#> ::debug::Taxonomy retrieved!
#> ::debug::Got OTTaxonomy!
#> ::debug::Keeping structures
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/merged/keys.tsv.gz
#> ::notice title=INFO::Directory data/interim/libraries/sop/merged/organisms/taxonomies created.
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/merged/organisms/taxonomies/ott.tsv.gz
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/merged/structures/stereo.tsv.gz
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/merged/structures/metadata.tsv.gz
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/merged/structures/names.tsv.gz
#> ::notice title=INFO::Directory data/interim/libraries/sop/merged/structures/taxonomies created.
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/merged/structures/taxonomies/classyfire.tsv.gz
#> ::notice title=INFO::... path to export is data/interim/libraries/sop/merged/structures/taxonomies/npc.tsv.gz
#> ✔ lib_sop_mer completed [1m 30.1s, 250 B]
#> + ann_spe_pos dispatched
#> ::debug::Loading spectra
#> ::notice title=INFO::Read 10000 spectra...
#> ::debug::Harmonizing names
#> ::debug::Filtering MS2 only
#> ::debug::Combining spectra in case
#> ::debug::Applying sanitization of the spectra
#> ::debug::Filtering empty spectra
#> ::notice title=INFO::Considering 3840 spectra
#> ::debug::Loading spectral libraries
#> ::debug::Harmonizing spectrum id
#> ::debug::Harmonizing spectrum id
#> ::debug::Harmonizing spectrum id
#> ::debug::Harmonizing spectrum id
#> ::debug::Harmonizing spectrum id
#> ::notice title=INFO::Annotating using following libraries
#> ::notice title=INFO::         library spectra unique_connectivities
#>  ISDB - Wikidata  998198                998198
#>             gnps  354788                 22675
#>           merlin  208273                 26197
#>         massbank   66388                  5901
#> ::debug::Reducing library size
#> ::debug::Annotating
#>  ■                                  1% |  ETA:  5m
#>  ■■                                 2% |  ETA:  5m
#>  ■■                                 3% |  ETA:  5m
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#>  ■■■■■■■■■                         26% |  ETA:  2m
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#>  ■■■■■■■■■■■                       33% |  ETA:  2m
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#>  ■■■■■■■■■■■■                      37% |  ETA:  2m
#>  ■■■■■■■■■■■■                      38% |  ETA:  2m
#>  ■■■■■■■■■■■■■                     40% |  ETA:  2m
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#>  ■■■■■■■■■■■■■■■■■■■■■■■           73% |  ETA: 47s
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#>  ■■■■■■■■■■■■■■■■■■■■■■■■          77% |  ETA: 39s
#>  ■■■■■■■■■■■■■■■■■■■■■■■■■         79% |  ETA: 36s
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#>  ■■■■■■■■■■■■■■■■■■■■■■■■■■        83% |  ETA: 29s
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#>  ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■    96% |  ETA:  7s
#>  ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■    98% |  ETA:  4s
#>  ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■  100% |  ETA:  1s
#> ::debug::Trying to harmonize adducts definitions
#> ::debug::Filtering results above threshold only
#> ::notice title=INFO::321348 Candidates were annotated on 3679 features, with at least 0 similarity score.
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/annotations/example_spectralMatches_pos.tsv.gz
#> ✔ ann_spe_pos completed [3m 51.5s, 37.54 MB]
#> + ann_spe_neg dispatched
#> ::debug::Loading spectra
#> ::notice title=INFO::Read 10000 spectra...
#> ::debug::Harmonizing names
#> ::debug::Filtering MS2 only
#> ::debug::Combining spectra in case
#> ::debug::Applying sanitization of the spectra
#> ::debug::Filtering empty spectra
#> ::notice title=INFO::Considering 0 spectra
#> ::warning title=WARN::No spectra matched the given polarity, returning an empty dataframe
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/annotations/example_spectralMatches_neg.tsv.gz
#> ✔ ann_spe_neg completed [8.3s, 187 B]
#> + edg_spe dispatched
#> ✔ edg_spe completed [0ms, 533.82 kB]
#> + lib_mer_key dispatched
#> ✔ lib_mer_key completed [0ms, 18.06 MB]
#> + lib_mer_str_met dispatched
#> ✔ lib_mer_str_met completed [0ms, 36.02 MB]
#> + lib_mer_str_nam dispatched
#> ✔ lib_mer_str_nam completed [1ms, 11.28 MB]
#> + lib_mer_str_stereo dispatched
#> ✔ lib_mer_str_stereo completed [0ms, 43.58 MB]
#> + lib_mer_str_tax_cla dispatched
#> ✔ lib_mer_str_tax_cla completed [1ms, 2.51 MB]
#> + lib_mer_str_tax_npc dispatched
#> ✔ lib_mer_str_tax_npc completed [0ms, 2.44 MB]
#> + lib_mer_org_tax_ott dispatched
#> ✔ lib_mer_org_tax_ott completed [0ms, 939.13 kB]
#> + ann_ms1_pre dispatched
#> ::debug::Filtering desired adducts and adding mz tolerance
#> ::notice title=INFO::Already 2112 adducts previously detected
#> ::debug::Trying to harmonize adducts definitions
#> ::debug::Calculating rt tolerance
#> ::debug::Joining within given rt tolerance
#> ::notice title=INFO::Here are the top 10 observed m/z differences inside the RT windows:
#> ::notice title=INFO::             bin   N
#>  (4.8501,5.0366] 352
#>  (21.822,22.009] 283
#>   (16.973,17.16] 208
#>  (17.906,18.092] 192
#>  (15.854,16.041] 172
#>    (39.914,40.1] 143
#>  (38.981,39.168] 137
#>  (34.878,35.065] 115
#>  (77.962,78.148] 114
#>  (1.8659,2.0524] 108
#> ::notice title=INFO::These differences may help identify potential preprocessing issues
#> ::debug::Forming adducts and clusters
#> ::debug::Calculating delta mz for single charge adducts and clusters
#> ::debug::Joining within given delta mz tolerance (neutral losses)
#> ::debug::Joining within given delta mz tolerance (adducts)
#> ::debug::Keeping initial and destination feature
#> ::debug::Joining with initial results (adducts)
#> ::debug::Joining with initial results (neutral losses)
#> ::debug::Joining within given mz tol to exact mass library
#> ::debug::Keeping unique exact masses and molecular formulas
#> ::debug::Joining exact masses with single charge adducts
#> ::debug::Getting back to M
#> ::debug::Calculating multicharged and in source dimers
#> ::debug::Joining within given rt tolerance
#> ::debug::Joining within given mz tol and filtering possible adducts
#> ::debug::Joining single adducts, in source dimers, and multicharged
#> ::debug::Adding chemical classification
#> ::notice title=INFO::MS1 annotation led to 48099 annotations on 4224 features
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/features/example_edgesMasses.tsv
#> ::notice title=INFO::... path to export is data/interim/annotations/example_ms1Prepared.tsv.gz
#> ✔ ann_ms1_pre completed [56s, 158 B]
#> + ann_spe_exp_gnp_pre dispatched
#> ::warning title=WARN::No GNPS annotations found, returning an empty file instead
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/annotations/example_gnpsPrepared.tsv.gz
#> ✔ ann_spe_exp_gnp_pre completed [20ms, 237 B]
#> + ann_spe_pre dispatched
#> ::debug::Loading and formatting spectral matches
#> ::debug::Selecting annotations columns
#> ::debug::Trying to look for already computed metadata
#> ::debug::Stereo loaded
#> ::debug::Metadata loaded
#> ::debug::Names loaded
#> ::debug::Classyfire done
#> ::debug::NPClassifier done
#> ::debug::Metadata done
#> ::debug::Names done
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/annotations/example_spectralMatchesPrepared.tsv.gz
#> ✔ ann_spe_pre completed [38.5s, 60.86 MB]
#> + ann_sir_pre dispatched
#> ::notice title=INFO::Loading parameters for SIRIUS 6
#> ::debug::Loading and formatting SIRIUS results...
#> ::debug::... CANOPUS loaded
#> ::debug::... formulas loaded
#> ::debug::... structures loaded
#> ::debug::... de novo loaded
#> ::debug::... CANOPUS prepared
#> ::debug::... formulas prepared
#> ::debug::... structures prepared
#> ::debug::... denovo prepared
#> ::debug::Everything joined together
#> ::debug::Selecting annotations columns
#> ::debug::Trying to look for already computed metadata
#> ::debug::Stereo loaded
#> ::debug::Metadata loaded
#> ::debug::Names loaded
#> ::debug::Classyfire done
#> ::debug::NPClassifier done
#> ::debug::Metadata done
#> ::debug::Names done
#> ::debug::Splitting SIRIUS results
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/annotations/example_canopusPrepared.tsv.gz
#> ::notice title=INFO::... path to export is data/interim/annotations/example_formulaPrepared.tsv.gz
#> ::notice title=INFO::... path to export is data/interim/annotations/example_siriusPrepared.tsv.gz
#> ✔ ann_sir_pre completed [18.1s, 165 B]
#> + tax_pre dispatched
#> ::debug::Loading feature table
#> ::debug::Loading metadata table
#> ::debug::Preparing organisms names
#> ::debug::Retrieving already computed Open Tree of Life Taxonomy
#> ::debug::Submitting the rest to OTL
#> ::debug::Testing if Open Tree of Life API is up
#> ::debug::Success! Submitting request
#> ::debug::Request finished!
#> ::notice title=INFO::Retrying with blk
#> ::debug::Getting taxonomy
#> ::debug::Taxonomy retrieved!
#> ::debug::Got OTTaxonomy!
#> ::debug::Joining all results
#> ::debug::Joining with metadata table
#> ::debug::Joining with cleaned taxonomy table
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::Directory data/interim/taxa created.
#> ::notice title=INFO::... path to export is data/interim/taxa/example_taxed.tsv.gz
#> ✔ tax_pre completed [1.8s, 19.70 kB]
#> + ann_ms1_pre_edg dispatched
#> ✔ ann_ms1_pre_edg completed [0ms, 81.71 kB]
#> + ann_ms1_pre_ann dispatched
#> ✔ ann_ms1_pre_ann completed [0ms, 10.81 MB]
#> + ann_sir_pre_can dispatched
#> ✔ ann_sir_pre_can completed [0ms, 784 B]
#> + ann_sir_pre_for dispatched
#> ✔ ann_sir_pre_for completed [0ms, 487 B]
#> + ann_sir_pre_str dispatched
#> ✔ ann_sir_pre_str completed [0ms, 24.42 kB]
#> + fea_edg_pre dispatched
#> ::debug::Loading edge table
#> ::debug::Formatting edge table
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/features/example_edges.tsv
#> ✔ fea_edg_pre completed [55ms, 758.28 kB]
#> + ann_fil dispatched
#> ::debug::... features
#> ::debug::... annotations
#> ::debug::Removing MS1 annotations for which we have spectral hits
#> ::debug::... retention times
#> ::notice title=INFO::Filtering annotations outside of Inf minutes tolerance
#> ::notice title=INFO::0 candidates were removed based on retention time.
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/annotations/example_annotationsFiltered.tsv.gz
#> ✔ ann_fil completed [15.6s, 56.07 MB]
#> + fea_com dispatched
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/features/example_components.tsv
#> ✔ fea_com completed [58ms, 51.39 kB]
#> + int_com dispatched
#> ✔ int_com completed [0ms, 51.39 kB]
#> + fea_com_pre dispatched
#> ::debug::Loading files
#> ::debug::Components table
#> ::notice title=INFO::... path to used parameters is data/interim/params
#> ::notice title=INFO::... path to export is data/interim/features/example_componentsPrepared.tsv
#> ✔ fea_com_pre completed [19ms, 51.38 kB]
#> + ann_pre dispatched
#> ::debug::Loading files ...
#> ::debug::... components
#> ::debug::... edges
#> ::debug::... structure-organism pairs
#> ::debug::... canopus
#> ::debug::... formula
#> ::debug::... annotations
#> ::debug::Initial annotations:
#> ::notice title=INFO:: candidate_library      n
#>    ISDB - Wikidata 577751
#>           TIMA MS1  82324
#>               gnps  25161
#>             merlin  23150
#>           massbank   3591
#>             SIRIUS    479
#> ::debug::Re-arranging annotations
#> ::debug::Adding biological organism metadata
#> ::debug::Performing taxonomically informed scoring
#> ::debug::Calculating biological score at all levels ...
#> ::debug::... domain
#> ::debug::... kingdom
#> ::debug::... phylum
#> ::debug::... class
#> ::debug::... order
#> ::debug::... family
#> ::debug::... tribe
#> ::debug::... genus
#> ::debug::... species
#> ::debug::... varietas
#> ::debug::Keeping best biological score
#> ::notice title=INFO::Taxonomically informed metabolite annotation led to 
#> 41238 annotations reranked at the kingdom level, 
#> 40784 annotations reranked at the phylum level, 
#> 35057 annotations reranked at the class level, 
#> 9353 annotations reranked at the order level, 
#> 7515 annotations reranked at the family level, 
#> 1184 annotations reranked at the tribe level, 
#> 919 annotations reranked at the genus level, 
#> 402 annotations reranked at the species level, and 
#> 0 annotations reranked at the variety level. 
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT! (for later predictions)
#> ::debug::Calculating chemical consistency of features with at least 2 neighbors
#> ::debug::Among all edges
#> ::debug::... at the (classyfire) kingdom level
#> ::debug::... at the (NPC) pathway level
#> ::debug::... at the (classyfire) superclass level
#> ::debug::... at the (NPC) superclass level
#> ::debug::... at the (classyfire) class level
#> ::debug::... at the (NPC) class level
#> ::debug::... at the (classyfire) parent level
#> ::debug::Splitting already computed predictions
#> ::debug::Joining all except -1 together
#> ::debug::Adding already computed predictions back
#> ::debug::Calculating chemical score at all levels ...
#> ::debug::... (classyfire) kingdom
#> ::debug::... (NPC) pathway
#> ::debug::... (classyfire) superclass
#> ::debug::... (NPC) superclass
#> ::debug::... (classyfire) class
#> ::debug::... (NPC) class
#> ::debug::... (classyfire) parent
#> ::debug::... keeping best chemical score
#> ::notice title=INFO::Chemically informed scoring led to 
#> 40464 annotations reranked at the (classyfire) kingdom level, 
#> 31334 annotations reranked at the (NPC) pathway level, 
#> 28047 annotations reranked at the (classyfire) superclass level, 
#> 23948 annotations reranked at the (NPC) superclass level, 
#> 28047 annotations reranked at the (classyfire) class level, 
#> 23948 annotations reranked at the (NPC) class level, and 
#> 23927 annotations reranked at the (classyfire) parent level. 
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT!
#> ::notice title=INFO::Filtering top 1 candidates and keeping only MS1 candidates with minimum 0 biological score OR 0 chemical score 
#> ::debug::Minimizing results
#> ::debug::Keeping high confidence candidates only
#> ::notice title=INFO::Removed 693032 low confidence candidates out of the 695221 total ones.
#> ::notice title=INFO::2189 high confidence candidates remaining.
#> ::debug::Processing full results
#> ::debug::Adding initial metadata (RT, etc.) and simplifying columns
#> ::debug::Selecting columns to export
#> ::debug::Adding consensus again to droped candidates
#> ::debug::Processing filtered results
#> ::debug::Adding initial metadata (RT, etc.) and simplifying columns
#> ::debug::Selecting columns to export
#> ::debug::Adding consensus again to droped candidates
#> ::notice title=INFO::Directory data/processed/20251027_102231_example created.
#> ::notice title=INFO::... path to used parameters is data/processed/20251027_102231_example
#> ::notice title=INFO::... path to used parameters is data/processed/20251027_102231_example
#> ::notice title=INFO::... path to export is data/processed/20251027_102231_example/example_results_mini.tsv
#> ::notice title=INFO::... path to export is data/processed/20251027_102231_example/example_results_filtered.tsv
#> ::notice title=INFO::... path to export is data/processed/20251027_102231_example/example_results.tsv
#> ✔ ann_pre completed [1m 29.3s, 3.97 MB]
#> ✔ ended pipeline [15m 33.5s, 126 completed, 0 skipped]
#> There were 14 warnings (use warnings() to see them)
#> Processing complete. Total molecules processed: 54
#> [1] TRUE

The final exported file is formatted in order to be easily imported in Cytoscape to further explore your data!

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Reuse

Citation

BibTeX citation:
@online{rutz2025,
  author = {Rutz, Adriano},
  title = {3 {Performing} {Taxonomically} {Informed} {Metabolite}
    {Annotation}},
  date = {2025-10-27},
  url = {https://taxonomicallyinformedannotation.github.io/tima/vignettes/articles/III-processing.html},
  langid = {en}
}
For attribution, please cite this work as:
Rutz, Adriano. 2025. “3 Performing Taxonomically Informed Metabolite Annotation.” October 27, 2025. https://taxonomicallyinformedannotation.github.io/tima/vignettes/articles/III-processing.html.