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Changeset 3:9dfcee100f48 (2023-05-25)

Previous changeset 2:86de39226109 (2023-05-18) Next changeset 4:0cf68b536cd1 (2023-06-27)

Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32

modified:
test-data/convert/json_out.json
test-data/convert/mgf_out.mgf
test-data/convert/msp_out.msp

added:
test-data/convert/harmonized_msp_out.msp
test-data/convert/harmonized_msp_peakcomments_out.msp

diff -r 86de39226109 -r 9dfcee100f48 test-data/convert/harmonized_msp_out.msp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/convert/harmonized_msp_out.msp Thu May 25 09:06:58 2023 +0000

[

b'@@ -0,0 +1,6548 @@\n+SCANNUMBER: 1161\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C4H10NO3PS\n+INCHIKEY: YASYVMFAVPKPKE-SECBINFHSA-N\n+INCHI: \n+SMILES: COP(=O)(N=C(O)C)SC\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Acephate\n+RETENTION_TIME: 1.232997\n+PRECURSOR_MZ: 184.0194\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 16\n+90.09368 1128.0\n+93.11512 1241.0\n+95.10279 1118.0\n+101.31465 1152.0\n+102.90688 1322.0\n+103.98039 1201.0\n+112.01607 12289.0\n+112.99994 38027.0\n+115.00399 1634.0\n+124.98121 922.0\n+128.97701 9208.0\n+132.57193 1350.0\n+135.84808 1428.0\n+142.99275 16419.0\n+147.94205 1750.0\n+173.5094 2353.0\n+\n+SCANNUMBER: 2257\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C12H11NO2\n+INCHIKEY: CVXBEEMKQHEXEN-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CN=C(Oc1cccc2c1cccc2)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Carbaryl\n+RETENTION_TIME: 5.259445\n+PRECURSOR_MZ: 202.0863\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 1\n+145.06491 1326147.0\n+\n+SCANNUMBER: 1516\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C8H16NO5P\n+INCHIKEY: VEENJGZXVHKXNB-UHFFFAOYSA-N\n+INCHI: \n+SMILES: COP(=O)(OC(=CC(=O)N(C)C)C)OC\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Dicrotophos\n+RETENTION_TIME: 2.025499\n+PRECURSOR_MZ: 238.0844\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 5\n+112.074 102027.0\n+112.07591 9070987.0\n+127.01563 3230337.0\n+193.02605 7897744.0\n+238.08437 2973124.0\n+\n+SCANNUMBER: 1865\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C5H12NO3PS2\n+INCHIKEY: MCWXGJITAZMZEV-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CN=C(CSP(=S)(OC)OC)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Dimethoate\n+RETENTION_TIME: 2.866696\n+PRECURSOR_MZ: 230.0072\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 8\n+88.0219 548446.0\n+124.98233 183861.0\n+142.99275 722053.0\n+156.95422 80792.0\n+170.97 1426256.0\n+197.98123 240915.0\n+198.96501 5415933.0\n+230.00722 497851.0\n+\n+SCANNUMBER: 3852\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C21H22NO4Cl\n+INCHIKEY: QNBTYORWCCMPQP-UHFFFAOYSA-N\n+INCHI: \n+SMILES: COc1cc(ccc1OC)C(=CC(=O)N1CCOCC1)c1ccc(cc1)Cl\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Dimethomorph\n+RETENTION_TIME: 7.060486\n+PRECURSOR_MZ: 388.1316\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 22\n+114.05532 468862.0\n+125.01571 886745.0\n+138.99484 4138370.0\n+155.0705 425164.0\n+165.05519 15513399.0\n+165.06543 350695.0\n+195.08057 386226.0\n+215.0262 490061.0\n+223.07544 702025.0\n+227.02576 230514.0\n+229.04225 216308.0\n+235.07555 241142.0\n+238.09914 1323577.0\n+242.04929 2449236.0\n+243.02142 891584.0\n+257.03726 578874.0\n+258.04443 3232295.0\n+266.0943 358273.0\n+270.04492 608851.0\n+273.06772 3866006.0\n+286.03912 483547.0\n+301.06311 4060551.0\n+\n+SCANNUMBER: 1009\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C2H8NO2PS\n+INCHIKEY: NNKVPIKMPCQWCG-ZCFIWIBFSA-N\n+INCHI: \n+SMILES: COP(=O)(SC)N\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Methamidophos\n+RETENTIO'..b': 2\n+86.0966 107829.0\n+102.05516 2507023.0\n+\n+SCANNUMBER: 711\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C11H15N3O2\n+INCHIKEY: MYPKGPZHHQEODQ-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Formetanate_1\n+RETENTION_TIME: 0.7730471\n+PRECURSOR_MZ: 222.1239\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 13\n+93.03365 1796.0\n+107.04935 1981.0\n+111.04435 82262.0\n+118.04142 1927.0\n+120.04462 150907.0\n+121.03984 67610.0\n+122.06016 5909.0\n+122.75254 1678.0\n+150.98424 1930.0\n+165.1024 143887.0\n+173.50876 2616.0\n+200.05632 2056.0\n+208.52768 2170.0\n+\n+SCANNUMBER: 1161\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C11H15N3O2\n+INCHIKEY: MYPKGPZHHQEODQ-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Formetanate_2\n+RETENTION_TIME: 1.13043\n+PRECURSOR_MZ: 222.1239\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 15\n+91.05441 6330.0\n+93.03365 27201.0\n+107.04935 4024.0\n+111.04435 131558.0\n+115.05429 3711.0\n+117.06996 5571.0\n+118.04177 4476.0\n+120.04462 274740.0\n+121.03984 113412.0\n+122.06016 7843.0\n+124.07605 4049.0\n+135.04427 4178.0\n+145.06488 3067.0\n+164.95049 3848.0\n+165.1024 263802.0\n+\n+SCANNUMBER: 1328\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C12H18N2O2\n+INCHIKEY: YNEVBPNZHBAYOA-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CN=C(Oc1cc(C)c(c(c1)C)N(C)C)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Mexacarbate\n+RETENTION_TIME: 1.682191\n+PRECURSOR_MZ: 223.1443\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 5\n+134.07283 2632951.0\n+136.07611 26036728.0\n+150.092 1572118.0\n+151.09932 54847764.0\n+166.12282 1541928.0\n+\n+SCANNUMBER: 3999\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C19H21N2OCl\n+INCHIKEY: OGYFATSSENRIKG-UHFFFAOYSA-N\n+INCHI: \n+SMILES: Clc1ccc(cc1)CN(C(=Nc1ccccc1)O)C1CCCC1\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Monceren\n+RETENTION_TIME: 7.14553\n+PRECURSOR_MZ: 329.1426\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 5\n+89.03881 550831.0\n+94.06543 635265.0\n+106.06545 446416.0\n+125.01307 512150.0\n+125.01532 37442116.0\n+\n+SCANNUMBER: 2271\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C16H16N2O4\n+INCHIKEY: WZJZMXBKUWKXTQ-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CCOC(=Nc1cccc(c1)OC(=Nc1ccccc1)O)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Desmedipham\n+RETENTION_TIME: 6.430396\n+PRECURSOR_MZ: 301.1192\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 3\n+136.03947 1773399.0\n+154.04993 1002798.0\n+182.08162 6480130.0\n+\n+SCANNUMBER: 2458\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C16H16N2O4\n+INCHIKEY: IDOWTHOLJBTAFI-UHFFFAOYSA-N\n+INCHI: \n+SMILES: COC(=Nc1cccc(c1)OC(=Nc1cccc(c1)C)O)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Phenmedipham\n+RETENTION_TIME: 6.570995\n+PRECURSOR_MZ: 301.1185\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 2\n+136.03947 2596929.0\n+168.06587 7038054.0\n+\n'

diff -r 86de39226109 -r 9dfcee100f48 test-data/convert/harmonized_msp_peakcomments_out.msp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/convert/harmonized_msp_peakcomments_out.msp Thu May 25 09:06:58 2023 +0000

[

b'@@ -0,0 +1,6548 @@\n+SCANNUMBER: 1161\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C4H10NO3PS\n+INCHIKEY: YASYVMFAVPKPKE-SECBINFHSA-N\n+INCHI: \n+SMILES: COP(=O)(N=C(O)C)SC\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Acephate\n+RETENTION_TIME: 1.232997\n+PRECURSOR_MZ: 184.0194\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 16\n+90.09368 1128.0\n+93.11512 1241.0\n+95.10279 1118.0\n+101.31465 1152.0\n+102.90688 1322.0\n+103.98039 1201.0\n+112.01607 12289.0\n+112.99994 38027.0\n+115.00399 1634.0\n+124.98121 922.0\n+128.97701 9208.0\n+132.57193 1350.0\n+135.84808 1428.0\n+142.99275 16419.0\n+147.94205 1750.0\n+173.5094 2353.0\n+\n+SCANNUMBER: 2257\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C12H11NO2\n+INCHIKEY: CVXBEEMKQHEXEN-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CN=C(Oc1cccc2c1cccc2)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Carbaryl\n+RETENTION_TIME: 5.259445\n+PRECURSOR_MZ: 202.0863\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 1\n+145.06491 1326147.0 "Theoretical m/z 145.064787, Mass diff 0 (0.85 ppm), SMILES OC1=CC=CC=2C=CC=CC12, Annotation [C10H8O+H]+, Rule of HR True"\n+\n+SCANNUMBER: 1516\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C8H16NO5P\n+INCHIKEY: VEENJGZXVHKXNB-UHFFFAOYSA-N\n+INCHI: \n+SMILES: COP(=O)(OC(=CC(=O)N(C)C)C)OC\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Dicrotophos\n+RETENTION_TIME: 2.025499\n+PRECURSOR_MZ: 238.0844\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 5\n+112.074 102027.0\n+112.07591 9070987.0 "Theoretical m/z 112.075687, Mass diff 0 (1.99 ppm), SMILES O=C(C=CC)N(C)C, Annotation [C6H11NO-H]+, Rule of HR True"\n+127.01563 3230337.0 "Theoretical m/z 127.01547, Mass diff 0 (1.26 ppm), SMILES O=P(O)(OC)OC, Annotation [C2H7O4P+H]+, Rule of HR True"\n+193.02605 7897744.0 "Theoretical m/z 193.026035, Mass diff 0 (0.08 ppm), SMILES O=CC=C(OP(=O)(OC)OC)C, Annotation [C6H11O5P-H]+, Rule of HR True"\n+238.08437 2973124.0 "Theoretical m/z 238.083891, Mass diff 0 (2.01 ppm), SMILES O=C(C=C(OP(=O)(OC)OC)C)N(C)C, Annotation [C8H16NO5P+H]+, Rule of HR True"\n+\n+SCANNUMBER: 1865\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C5H12NO3PS2\n+INCHIKEY: MCWXGJITAZMZEV-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CN=C(CSP(=S)(OC)OC)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Dimethoate\n+RETENTION_TIME: 2.866696\n+PRECURSOR_MZ: 230.0072\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 8\n+88.0219 548446.0 "Theoretical m/z 88.021549, Mass diff 0 (3.99 ppm), SMILES SCC=NC, Annotation [C3H7NS-H]+, Rule of HR True"\n+124.98233 183861.0 "Theoretical m/z 124.982067, Mass diff 0 (2.11 ppm), SMILES S=P(OC)OC, Annotation [C2H7O2PS-H]+, Rule of HR True"\n+142.99275 722053.0 "Theoretical m/z 142.993177, Mass diff 0 (0 ppm), Formula C2H8O3PS"\n+156.95422 80792.0 "Theoretical m/z 156.954136, Mass diff 0 (0.54 ppm), SMILES S=P(S)(OC)OC, Annotation [C2H7O2PS2-H]+, Rule of HR True"\n+170.97 1426256.0 "Theoretical m/z 170.969791, Mass diff 0 (1.22 ppm), SMILES S=P(OC)(OC)SC, Annotation [C3H9O2PS2-H]+, Rule of HR True"\n+197.98123 240915.0 "Theoretical m/z 197.980686, Mass diff 0.001 (2.75 ppm), SMILES S=P(OC)SCC(O)=NC, Annotation [C4H10NO2PS2-H]+, Rule of HR True"\n+198.96501 5415933.0 "Theoretical m/z 198.965248, Mass diff 0 (0 ppm), Formula C4H8O3PS2"\n+230.00722 497851.0 '..b'ORMULA: C12H18N2O2\n+INCHIKEY: YNEVBPNZHBAYOA-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CN=C(Oc1cc(C)c(c(c1)C)N(C)C)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Mexacarbate\n+RETENTION_TIME: 1.682191\n+PRECURSOR_MZ: 223.1443\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 5\n+134.07283 2632951.0 "Theoretical m/z 134.072623, Mass diff 0 (1.55 ppm), SMILES O(C=1C=C(C=C(C1)C)C)C, Annotation [C9H12O-2H]+, Rule of HR False"\n+136.07611 26036728.0 "Theoretical m/z 136.076239, Mass diff 0 (0 ppm), Formula C8H10NO"\n+150.092 1572118.0 "Theoretical m/z 150.091343, Mass diff 0.001 (4.38 ppm), SMILES OC1=CC=C(C(=C1)C)N(C)C, Annotation [C9H13NO-H]+, Rule of HR True"\n+151.09932 54847764.0 "Theoretical m/z 151.099168, Mass diff 0 (1.01 ppm), SMILES OC1=CC=C(C(=C1)C)N(C)C, Annotation [C9H13NO]+, Rule of HR False"\n+166.12282 1541928.0 "Theoretical m/z 166.122633, Mass diff 0 (1.13 ppm), SMILES OC=1C=C(C(=C(C1)C)N(C)C)C, Annotation [C10H15NO+H]+, Rule of HR True"\n+\n+SCANNUMBER: 3999\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C19H21N2OCl\n+INCHIKEY: OGYFATSSENRIKG-UHFFFAOYSA-N\n+INCHI: \n+SMILES: Clc1ccc(cc1)CN(C(=Nc1ccccc1)O)C1CCCC1\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Monceren\n+RETENTION_TIME: 7.14553\n+PRECURSOR_MZ: 329.1426\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 5\n+89.03881 550831.0 "Theoretical m/z 89.038575, Mass diff 0 (2.63 ppm), SMILES C=1C=CC(=CC1)C, Annotation [C7H8-3H]+, Rule of HR True"\n+94.06543 635265.0 "Theoretical m/z 94.065123, Mass diff 0 (3.27 ppm), SMILES NC=1C=CC=CC1, Annotation [C6H7N+H]+, Rule of HR True"\n+106.06545 446416.0 "Theoretical m/z 106.065123, Mass diff 0 (3.09 ppm), SMILES N(=C)C=1C=CC=CC1, Annotation [C7H7N+H]+, Rule of HR True"\n+125.01307 512150.0\n+125.01532 37442116.0 "Theoretical m/z 125.015255, Mass diff 0 (0.52 ppm), SMILES ClC1=CC=C(C=C1)C, Annotation [C7H7Cl-H]+, Rule of HR True"\n+\n+SCANNUMBER: 2271\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C16H16N2O4\n+INCHIKEY: WZJZMXBKUWKXTQ-UHFFFAOYSA-N\n+INCHI: \n+SMILES: CCOC(=Nc1cccc(c1)OC(=Nc1ccccc1)O)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Desmedipham\n+RETENTION_TIME: 6.430396\n+PRECURSOR_MZ: 301.1192\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 3\n+136.03947 1773399.0 "Theoretical m/z 136.03931, Mass diff 0 (1.18 ppm), SMILES OC(O)=NC=1C=CC=CC1, Annotation [C7H7NO2-H]+, Rule of HR True"\n+154.04993 1002798.0 "Theoretical m/z 154.049864, Mass diff 0 (0.43 ppm), SMILES OC(O)=NC=1C=CC=C(O)C1, Annotation [C7H7NO3+H]+, Rule of HR True"\n+182.08162 6480130.0 "Theoretical m/z 182.081175, Mass diff 0 (2.45 ppm), SMILES OC(=NC=1C=CC=C(O)C1)OCC, Annotation [C9H11NO3+H]+, Rule of HR True"\n+\n+SCANNUMBER: 2458\n+IONMODE: positive\n+SPECTRUMTYPE: Centroid\n+FORMULA: C16H16N2O4\n+INCHIKEY: IDOWTHOLJBTAFI-UHFFFAOYSA-N\n+INCHI: \n+SMILES: COC(=Nc1cccc(c1)OC(=Nc1cccc(c1)C)O)O\n+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n+INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n+IONIZATION: ESI+\n+LICENSE: CC BY-NC\n+COMMENT: \n+COMPOUND_NAME: Phenmedipham\n+RETENTION_TIME: 6.570995\n+PRECURSOR_MZ: 301.1185\n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n+NUM PEAKS: 2\n+136.03947 2596929.0 "Theoretical m/z 136.03931, Mass diff 0 (1.18 ppm), SMILES OC(O)=NC=1C=CC=CC1, Annotation [C7H7NO2-H]+, Rule of HR True"\n+168.06587 7038054.0 "Theoretical m/z 168.065519, Mass diff 0 (2.09 ppm), SMILES OC(=NC=1C=CC=C(O)C1)OC, Annotation [C8H9NO3+H]+, Rule of HR True"\n+\n'

diff -r 86de39226109 -r 9dfcee100f48 test-data/convert/json_out.json
--- a/test-data/convert/json_out.json Thu May 18 13:24:40 2023 +0000
+++ b/test-data/convert/json_out.json Thu May 25 09:06:58 2023 +0000

[

b'@@ -1,1 +1,1 @@\n-[{"scannumber": "1161", "precursortype": "[M+H]+", "ionmode": "Positive", "spectrumtype": "Centroid", "formula": "C4H10NO3PS", "inchikey": "YASYVMFAVPKPKE-SECBINFHSA-N", "inchi": "", "smiles": "COP(=O)(N=C(O)C)SC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "instrumenttype": "LC-ESI-Orbitrap", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "num_peaks": "16", "compound_name": "Acephate", "retention_time": "1.232997", "precursor_mz": "184.0194", "collision_energy": "", "peaks_json": [[90.09368, 1128.0], [93.11512, 1241.0], [95.10279, 1118.0], [101.31465, 1152.0], [102.90688, 1322.0], [103.98039, 1201.0], [112.01607, 12289.0], [112.99994, 38027.0], [115.00399, 1634.0], [124.98121, 922.0], [128.97701, 9208.0], [132.57193, 1350.0], [135.84808, 1428.0], [142.99275, 16419.0], [147.94205, 1750.0], [173.5094, 2353.0]]}, {"scannumber": "2257", "precursortype": "[M+H]+", "ionmode": "Positive", "spectrumtype": "Centroid", "formula": "C12H11NO2", "inchikey": "CVXBEEMKQHEXEN-UHFFFAOYSA-N", "inchi": "", "smiles": "CN=C(Oc1cccc2c1cccc2)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "instrumenttype": "LC-ESI-Orbitrap", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"145.06491": "Theoretical m/z 145.064787, Mass diff 0 (0.85 ppm), SMILES OC1=CC=CC=2C=CC=CC12, Annotation [C10H8O+H]+, Rule of HR True"}, "num_peaks": "1", "compound_name": "Carbaryl", "retention_time": "5.259445", "precursor_mz": "202.0863", "collision_energy": "", "peaks_json": [[145.06491, 1326147.0]]}, {"scannumber": "1516", "precursortype": "[M+H]+", "ionmode": "Positive", "spectrumtype": "Centroid", "formula": "C8H16NO5P", "inchikey": "VEENJGZXVHKXNB-UHFFFAOYSA-N", "inchi": "", "smiles": "COP(=O)(OC(=CC(=O)N(C)C)C)OC", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "instrumenttype": "LC-ESI-Orbitrap", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"112.07591": "Theoretical m/z 112.075687, Mass diff 0 (1.99 ppm), SMILES O=C(C=CC)N(C)C, Annotation [C6H11NO-H]+, Rule of HR True", "127.01563": "Theoretical m/z 127.01547, Mass diff 0 (1.26 ppm), SMILES O=P(O)(OC)OC, Annotation [C2H7O4P+H]+, Rule of HR True", "193.02605": "Theoretical m/z 193.026035, Mass diff 0 (0.08 ppm), SMILES O=CC=C(OP(=O)(OC)OC)C, Annotation [C6H11O5P-H]+, Rule of HR True", "238.08437": "Theoretical m/z 238.083891, Mass diff 0 (2.01 ppm), SMILES O=C(C=C(OP(=O)(OC)OC)C)N(C)C, Annotation [C8H16NO5P+H]+, Rule of HR True"}, "num_peaks": "5", "compound_name": "Dicrotophos", "retention_time": "2.025499", "precursor_mz": "238.0844", "collision_energy": "", "peaks_json": [[112.074, 102027.0], [112.07591, 9070987.0], [127.01563, 3230337.0], [193.02605, 7897744.0], [238.08437, 2973124.0]]}, {"scannumber": "1865", "precursortype": "[M+H]+", "ionmode": "Positive", "spectrumtype": "Centroid", "formula": "C5H12NO3PS2", "inchikey": "MCWXGJITAZMZEV-UHFFFAOYSA-N", "inchi": "", "smiles": "CN=C(CSP(=S)(OC)OC)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "instrumenttype": "LC-ESI-Orbitrap", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"88.0219": "Theoretical m/z 88.021549, Mass diff 0 (3.99 ppm), SMILES SCC=NC, Annotation [C3H7NS-H]+, Rule of HR True", "124.98233": "Theoretical m/z 124.982067, Mass diff 0 (2.11 ppm), SMILES S=P(OC)OC, Annotation [C2H7O2PS-H]+, Rule of HR True", "142.99275": "Theoretical m/z 142.993177, Mass diff 0 (0 ppm), Formula C2H8O3PS", "156.95422": "Theoretical m/z 156.954136, Mass diff 0 (0.54 ppm), SMILES S=P(S)(OC)OC, Annotation [C2H7O2PS2-H]+, Rule of HR True", "170.97": "Theoretical m/z 170.969791, Mass diff 0 (1.22 ppm), SMILES S=P(OC)(OC)SC, '..b'C(=C1)C)N(C)C, Annotation [C9H13NO-H]+, Rule of HR True", "151.09932": "Theoretical m/z 151.099168, Mass diff 0 (1.01 ppm), SMILES OC1=CC=C(C(=C1)C)N(C)C, Annotation [C9H13NO]+, Rule of HR False", "166.12282": "Theoretical m/z 166.122633, Mass diff 0 (1.13 ppm), SMILES OC=1C=C(C(=C(C1)C)N(C)C)C, Annotation [C10H15NO+H]+, Rule of HR True"}, "num_peaks": "5", "compound_name": "Mexacarbate", "retention_time": "1.682191", "precursor_mz": "223.1443", "adduct": "[M+H]+", "collision_energy": "", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[134.07283, 2632951.0], [136.07611, 26036728.0], [150.092, 1572118.0], [151.09932, 54847764.0], [166.12282, 1541928.0]]}, {"scannumber": "3999", "ionmode": "Positive", "spectrumtype": "Centroid", "formula": "C19H21N2OCl", "inchikey": "OGYFATSSENRIKG-UHFFFAOYSA-N", "inchi": "", "smiles": "Clc1ccc(cc1)CN(C(=Nc1ccccc1)O)C1CCCC1", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"89.03881": "Theoretical m/z 89.038575, Mass diff 0 (2.63 ppm), SMILES C=1C=CC(=CC1)C, Annotation [C7H8-3H]+, Rule of HR True", "94.06543": "Theoretical m/z 94.065123, Mass diff 0 (3.27 ppm), SMILES NC=1C=CC=CC1, Annotation [C6H7N+H]+, Rule of HR True", "106.06545": "Theoretical m/z 106.065123, Mass diff 0 (3.09 ppm), SMILES N(=C)C=1C=CC=CC1, Annotation [C7H7N+H]+, Rule of HR True", "125.01532": "Theoretical m/z 125.015255, Mass diff 0 (0.52 ppm), SMILES ClC1=CC=C(C=C1)C, Annotation [C7H7Cl-H]+, Rule of HR True"}, "num_peaks": "5", "compound_name": "Monceren", "retention_time": "7.14553", "precursor_mz": "329.1426", "adduct": "[M+H]+", "collision_energy": "", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[89.03881, 550831.0], [94.06543, 635265.0], [106.06545, 446416.0], [125.01307, 512150.0], [125.01532, 37442116.0]]}, {"scannumber": "2271", "ionmode": "Positive", "spectrumtype": "Centroid", "formula": "C16H16N2O4", "inchikey": "WZJZMXBKUWKXTQ-UHFFFAOYSA-N", "inchi": "", "smiles": "CCOC(=Nc1cccc(c1)OC(=Nc1ccccc1)O)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"136.03947": "Theoretical m/z 136.03931, Mass diff 0 (1.18 ppm), SMILES OC(O)=NC=1C=CC=CC1, Annotation [C7H7NO2-H]+, Rule of HR True", "154.04993": "Theoretical m/z 154.049864, Mass diff 0 (0.43 ppm), SMILES OC(O)=NC=1C=CC=C(O)C1, Annotation [C7H7NO3+H]+, Rule of HR True", "182.08162": "Theoretical m/z 182.081175, Mass diff 0 (2.45 ppm), SMILES OC(=NC=1C=CC=C(O)C1)OCC, Annotation [C9H11NO3+H]+, Rule of HR True"}, "num_peaks": "3", "compound_name": "Desmedipham", "retention_time": "6.430396", "precursor_mz": "301.1192", "adduct": "[M+H]+", "collision_energy": "", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[136.03947, 1773399.0], [154.04993, 1002798.0], [182.08162, 6480130.0]]}, {"scannumber": "2458", "ionmode": "Positive", "spectrumtype": "Centroid", "formula": "C16H16N2O4", "inchikey": "IDOWTHOLJBTAFI-UHFFFAOYSA-N", "inchi": "", "smiles": "COC(=Nc1cccc(c1)OC(=Nc1cccc(c1)C)O)O", "authors": "Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)", "instrument": "LC Orbitrap Fusion Tribrid MS", "ionization": "ESI+", "license": "CC BY-NC", "comment": "", "peak_comments": {"136.03947": "Theoretical m/z 136.03931, Mass diff 0 (1.18 ppm), SMILES OC(O)=NC=1C=CC=CC1, Annotation [C7H7NO2-H]+, Rule of HR True", "168.06587": "Theoretical m/z 168.065519, Mass diff 0 (2.09 ppm), SMILES OC(=NC=1C=CC=C(O)C1)OC, Annotation [C8H9NO3+H]+, Rule of HR True"}, "num_peaks": "2", "compound_name": "Phenmedipham", "retention_time": "6.570995", "precursor_mz": "301.1185", "adduct": "[M+H]+", "collision_energy": "", "instrument_type": "LC-ESI-Orbitrap", "peaks_json": [[136.03947, 2596929.0], [168.06587, 7038054.0]]}]\n\\ No newline at end of file\n'

diff -r 86de39226109 -r 9dfcee100f48 test-data/convert/mgf_out.mgf
--- a/test-data/convert/mgf_out.mgf Thu May 18 13:24:40 2023 +0000
+++ b/test-data/convert/mgf_out.mgf Thu May 25 09:06:58 2023 +0000

[

b'@@ -1,6 +1,5 @@\n BEGIN IONS\n SCANNUMBER=1161\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C4H10NO3PS\n@@ -9,7 +8,6 @@\n SMILES=COP(=O)(N=C(O)C)SC\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -17,7 +15,9 @@\n COMPOUND_NAME=Acephate\n RETENTION_TIME=1.232997\n PRECURSOR_MZ=184.0194\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 90.09368 1128.0 \n 93.11512 1241.0 \n 95.10279 1118.0 \n@@ -38,7 +38,6 @@\n \n BEGIN IONS\n SCANNUMBER=2257\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C12H11NO2\n@@ -47,7 +46,6 @@\n SMILES=CN=C(Oc1cccc2c1cccc2)O\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -56,13 +54,14 @@\n COMPOUND_NAME=Carbaryl\n RETENTION_TIME=5.259445\n PRECURSOR_MZ=202.0863\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 145.06491 1326147.0 \n END IONS\n \n BEGIN IONS\n SCANNUMBER=1516\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C8H16NO5P\n@@ -71,7 +70,6 @@\n SMILES=COP(=O)(OC(=CC(=O)N(C)C)C)OC\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -80,7 +78,9 @@\n COMPOUND_NAME=Dicrotophos\n RETENTION_TIME=2.025499\n PRECURSOR_MZ=238.0844\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 112.074 102027.0 \n 112.07591 9070987.0 \n 127.01563 3230337.0 \n@@ -90,7 +90,6 @@\n \n BEGIN IONS\n SCANNUMBER=1865\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C5H12NO3PS2\n@@ -99,7 +98,6 @@\n SMILES=CN=C(CSP(=S)(OC)OC)O\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -108,7 +106,9 @@\n COMPOUND_NAME=Dimethoate\n RETENTION_TIME=2.866696\n PRECURSOR_MZ=230.0072\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 88.0219 548446.0 \n 124.98233 183861.0 \n 142.99275 722053.0 \n@@ -121,7 +121,6 @@\n \n BEGIN IONS\n SCANNUMBER=3852\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C21H22NO4Cl\n@@ -130,7 +129,6 @@\n SMILES=COc1cc(ccc1OC)C(=CC(=O)N1CCOCC1)c1ccc(cc1)Cl\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -139,7 +137,9 @@\n COMPOUND_NAME=Dimethomorph\n RETENTION_TIME=7.060486\n PRECURSOR_MZ=388.1316\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 114.05532 468862.0 \n 125.01571 886745.0 \n 138.99484 4138370.0 \n@@ -166,7 +166,6 @@\n \n BEGIN IONS\n SCANNUMBER=1009\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C2H8NO2PS\n@@ -175,7 +174,6 @@\n SMILES=COP(=O)(SC)N\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -184,7 +182,9 @@\n COMPOUND_NAME=Methamidophos\n RETENTION_TIME=1.153307\n PRECURSOR_MZ=142.0089\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 98.00042 37721.0 \n 109.98272 71172.0 \n 112.01607 2867923.0 \n@@ -193,7 +193,6 @@\n \n BEGIN IONS\n SCANNUMBER=1924\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C7H13O6P\n@@ -202,7 +201,6 @@\n SMILES=COC(=O)C=C(OP(=O)(OC)OC)C\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-O'..b'opamocarb_2\n RETENTION_TIME=1.081971\n PRECURSOR_MZ=189.1603\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 86.0966 107829.0 \n 102.05516 2507023.0 \n END IONS\n \n BEGIN IONS\n SCANNUMBER=711\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C11H15N3O2\n@@ -6885,7 +6884,6 @@\n SMILES=CN=C(Oc1cccc(c1)N=CN(C)C)O\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -6894,7 +6892,9 @@\n COMPOUND_NAME=Formetanate_1\n RETENTION_TIME=0.7730471\n PRECURSOR_MZ=222.1239\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 93.03365 1796.0 \n 107.04935 1981.0 \n 111.04435 82262.0 \n@@ -6912,7 +6912,6 @@\n \n BEGIN IONS\n SCANNUMBER=1161\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C11H15N3O2\n@@ -6921,7 +6920,6 @@\n SMILES=CN=C(Oc1cccc(c1)N=CN(C)C)O\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -6930,7 +6928,9 @@\n COMPOUND_NAME=Formetanate_2\n RETENTION_TIME=1.13043\n PRECURSOR_MZ=222.1239\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 91.05441 6330.0 \n 93.03365 27201.0 \n 107.04935 4024.0 \n@@ -6950,7 +6950,6 @@\n \n BEGIN IONS\n SCANNUMBER=1328\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C12H18N2O2\n@@ -6959,7 +6958,6 @@\n SMILES=CN=C(Oc1cc(C)c(c(c1)C)N(C)C)O\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -6968,7 +6966,9 @@\n COMPOUND_NAME=Mexacarbate\n RETENTION_TIME=1.682191\n PRECURSOR_MZ=223.1443\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 134.07283 2632951.0 \n 136.07611 26036728.0 \n 150.092 1572118.0 \n@@ -6978,7 +6978,6 @@\n \n BEGIN IONS\n SCANNUMBER=3999\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C19H21N2OCl\n@@ -6987,7 +6986,6 @@\n SMILES=Clc1ccc(cc1)CN(C(=Nc1ccccc1)O)C1CCCC1\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -6996,7 +6994,9 @@\n COMPOUND_NAME=Monceren\n RETENTION_TIME=7.14553\n PRECURSOR_MZ=329.1426\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 89.03881 550831.0 \n 94.06543 635265.0 \n 106.06545 446416.0 \n@@ -7006,7 +7006,6 @@\n \n BEGIN IONS\n SCANNUMBER=2271\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C16H16N2O4\n@@ -7015,7 +7014,6 @@\n SMILES=CCOC(=Nc1cccc(c1)OC(=Nc1ccccc1)O)O\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -7024,7 +7022,9 @@\n COMPOUND_NAME=Desmedipham\n RETENTION_TIME=6.430396\n PRECURSOR_MZ=301.1192\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 136.03947 1773399.0 \n 154.04993 1002798.0 \n 182.08162 6480130.0 \n@@ -7032,7 +7032,6 @@\n \n BEGIN IONS\n SCANNUMBER=2458\n-PRECURSORTYPE=[M+H]+\n IONMODE=Positive\n SPECTRUMTYPE=Centroid\n FORMULA=C16H16N2O4\n@@ -7041,7 +7040,6 @@\n SMILES=COC(=Nc1cccc(c1)OC(=Nc1cccc(c1)C)O)O\n AUTHORS=Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT=LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE=LC-ESI-Orbitrap\n IONIZATION=ESI+\n LICENSE=CC BY-NC\n COMMENT=\n@@ -7050,7 +7048,9 @@\n COMPOUND_NAME=Phenmedipham\n RETENTION_TIME=6.570995\n PRECURSOR_MZ=301.1185\n-COLLISION_ENERGY=\n+ADDUCT=[M+H]+\n+COLLISION_ENERGY=\n+INSTRUMENT_TYPE=LC-ESI-Orbitrap\n 136.03947 2596929.0 \n 168.06587 7038054.0 \n END IONS\n'

diff -r 86de39226109 -r 9dfcee100f48 test-data/convert/msp_out.msp
--- a/test-data/convert/msp_out.msp Thu May 18 13:24:40 2023 +0000
+++ b/test-data/convert/msp_out.msp Thu May 25 09:06:58 2023 +0000

[

b'@@ -1,5 +1,4 @@\n SCANNUMBER: 1161\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C4H10NO3PS\n@@ -8,14 +7,15 @@\n SMILES: COP(=O)(N=C(O)C)SC\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Acephate\n RETENTION_TIME: 1.232997\n PRECURSOR_MZ: 184.0194\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 16\n 90.09368 1128.0\n 93.11512 1241.0\n@@ -35,7 +35,6 @@\n 173.5094 2353.0\n \n SCANNUMBER: 2257\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C12H11NO2\n@@ -44,19 +43,19 @@\n SMILES: CN=C(Oc1cccc2c1cccc2)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Carbaryl\n RETENTION_TIME: 5.259445\n PRECURSOR_MZ: 202.0863\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 1\n 145.06491 1326147.0\n \n SCANNUMBER: 1516\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C8H16NO5P\n@@ -65,14 +64,15 @@\n SMILES: COP(=O)(OC(=CC(=O)N(C)C)C)OC\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Dicrotophos\n RETENTION_TIME: 2.025499\n PRECURSOR_MZ: 238.0844\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 112.074 102027.0\n 112.07591 9070987.0\n@@ -81,7 +81,6 @@\n 238.08437 2973124.0\n \n SCANNUMBER: 1865\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C5H12NO3PS2\n@@ -90,14 +89,15 @@\n SMILES: CN=C(CSP(=S)(OC)OC)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Dimethoate\n RETENTION_TIME: 2.866696\n PRECURSOR_MZ: 230.0072\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 8\n 88.0219 548446.0\n 124.98233 183861.0\n@@ -109,7 +109,6 @@\n 230.00722 497851.0\n \n SCANNUMBER: 3852\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C21H22NO4Cl\n@@ -118,14 +117,15 @@\n SMILES: COc1cc(ccc1OC)C(=CC(=O)N1CCOCC1)c1ccc(cc1)Cl\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Dimethomorph\n RETENTION_TIME: 7.060486\n PRECURSOR_MZ: 388.1316\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 22\n 114.05532 468862.0\n 125.01571 886745.0\n@@ -151,7 +151,6 @@\n 301.06311 4060551.0\n \n SCANNUMBER: 1009\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C2H8NO2PS\n@@ -160,14 +159,15 @@\n SMILES: COP(=O)(SC)N\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Methamidophos\n RETENTION_TIME: 1.153307\n PRECURSOR_MZ: 142.0089\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 4\n 98.00042 37721.0\n 109.98272 71172.0\n@@ -175,7 +175,6 @@\n 127.99321 75837.0\n \n SCANNUMBER: 1924\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C7H13O6P\n@@ -184,14 +183,15 @@\n SMILES: COC(=O)C=C(OP(=O)(OC)OC)C\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion T'..b'NTION_TIME: 1.081971\n PRECURSOR_MZ: 189.1603\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 2\n 86.0966 107829.0\n 102.05516 2507023.0\n \n SCANNUMBER: 711\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C11H15N3O2\n@@ -6393,14 +6392,15 @@\n SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Formetanate_1\n RETENTION_TIME: 0.7730471\n PRECURSOR_MZ: 222.1239\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 13\n 93.03365 1796.0\n 107.04935 1981.0\n@@ -6417,7 +6417,6 @@\n 208.52768 2170.0\n \n SCANNUMBER: 1161\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C11H15N3O2\n@@ -6426,14 +6425,15 @@\n SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Formetanate_2\n RETENTION_TIME: 1.13043\n PRECURSOR_MZ: 222.1239\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 15\n 91.05441 6330.0\n 93.03365 27201.0\n@@ -6452,7 +6452,6 @@\n 165.1024 263802.0\n \n SCANNUMBER: 1328\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C12H18N2O2\n@@ -6461,14 +6460,15 @@\n SMILES: CN=C(Oc1cc(C)c(c(c1)C)N(C)C)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Mexacarbate\n RETENTION_TIME: 1.682191\n PRECURSOR_MZ: 223.1443\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 134.07283 2632951.0\n 136.07611 26036728.0\n@@ -6477,7 +6477,6 @@\n 166.12282 1541928.0\n \n SCANNUMBER: 3999\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C19H21N2OCl\n@@ -6486,14 +6485,15 @@\n SMILES: Clc1ccc(cc1)CN(C(=Nc1ccccc1)O)C1CCCC1\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Monceren\n RETENTION_TIME: 7.14553\n PRECURSOR_MZ: 329.1426\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 5\n 89.03881 550831.0\n 94.06543 635265.0\n@@ -6502,7 +6502,6 @@\n 125.01532 37442116.0\n \n SCANNUMBER: 2271\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C16H16N2O4\n@@ -6511,21 +6510,21 @@\n SMILES: CCOC(=Nc1cccc(c1)OC(=Nc1ccccc1)O)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Desmedipham\n RETENTION_TIME: 6.430396\n PRECURSOR_MZ: 301.1192\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 3\n 136.03947 1773399.0\n 154.04993 1002798.0\n 182.08162 6480130.0\n \n SCANNUMBER: 2458\n-PRECURSORTYPE: [M+H]+\n IONMODE: Positive\n SPECTRUMTYPE: Centroid\n FORMULA: C16H16N2O4\n@@ -6534,14 +6533,15 @@\n SMILES: COC(=Nc1cccc(c1)OC(=Nc1cccc(c1)C)O)O\n AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)\n INSTRUMENT: LC Orbitrap Fusion Tribrid MS\n-INSTRUMENTTYPE: LC-ESI-Orbitrap\n IONIZATION: ESI+\n LICENSE: CC BY-NC\n COMMENT: \n COMPOUND_NAME: Phenmedipham\n RETENTION_TIME: 6.570995\n PRECURSOR_MZ: 301.1185\n-COLLISION_ENERGY: \n+ADDUCT: [M+H]+\n+COLLISION_ENERGY: \n+INSTRUMENT_TYPE: LC-ESI-Orbitrap\n NUM PEAKS: 2\n 136.03947 2596929.0\n 168.06587 7038054.0\n'