Supporting Information for Publication Mass spectrometry-based untargeted metabolomics reveals the importance of glycosylated flavones in lentil seed coat patterns. Fatma M. Elessawy,1 Derek Wright,2 Albert Vandenberg,2 Anas El-Aneed,1 and Randy W. Purves 1,2,3,* 1College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada 2Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada 3Centre for Veterinary Drug Residues, Canadian Food Inspection Agency, Saskatoon, SK, Canada *Corresponding author Email address: randy.purves@usask.ca or randy.purves@inspection.gc.ca, Tel: +1 306-385-7843 mailto:randy.purves@usask.ca mailto:randy.purves@inspection.gc.ca Supporting Information for Publication Table S1. List of polyphenols, including subclasses and supplier (& country) for the standards used in creating the mzVault library. Labelled internal standards (IS) are indicated in bold. Compound name Supplier (Country) Anthocyanins Pelargonidin 3-O-glucoside Extrasynthese, France Malvidin 3-O-glucoside (oenin) Extrasynthese, France Pelargonidin 3,5-di-O-glucoside Extrasynthese, France Peonidin 3,5-di-O-glucoside Extrasynthese, France Peonidin 3-O-glucoside Extrasynthese, France Cyanidin 3,5-di-O-glucoside Extrasynthese, France Cyanidin 3-O-rhamnoside Extrasynthese, France Delphinidin 3,5-di-O-glucoside Extrasynthese, France Delphinidin 3-O-rhamnoside Extrasynthese, France Delphinidin 3-β-D-Glucoside Santa Cruz Biotech, USA Cyanidin 3-O-glucoside Extrasynthese, France Malvidin 3,5-di-O-glucoside Extrasynthese, France Malvidin 3-O-galactoside Extrasynthese, France Cyanidin 3-O-rutinoside Extrasynthese, France Peonidin 3-O-rutinoside Extrasynthese, France Delphinidin 3-O-rutinoside Extrasynthese, France Pelargonidin 3-O-rutinoside Extrasynthese, France Chalcones Phloretin Sigma Aldrich, USA Xanthohumol Extrasynthese, France Hydroxycoumarins 4-Hydroxy-6-methylcoumarin Sigma Aldrich, USA Flavonols Kaempferol-3-O-rhamnoside Sigma Aldrich, USA Fisetin Extrasynthese, France Isorhamnetin Sigma Aldrich, USA Kaempferol Sigma Aldrich, USA Kaempferol 3-O-robinoside-7-O-rhamnoside (robinin) Sigma Aldrich, USA Kaempferol 3-O-rutinoside-4'-glucoside Sigma Aldrich, USA Kaempferol-3-O-D-galactoside Sigma Aldrich, USA Kaempferol-3-O-glucoside Extrasynthese, France Kaempferol-3-O-rutinoside Extrasynthese, France Supporting Information for Publication Kaempferol-7-O-glucoside Extrasynthese, France Kaempferol-7-O-neohesperidoside Extrasynthese, France Myricetin Sigma Aldrich, USA Myricetin-3-O-rhamnoside Extrasynthese, France Quercetin Extrasynthese, France Quercetin-3,4'-di-O-glucoside Extrasynthese, France Quercetin-3-O-galactoside Extrasynthese, France Quercetin-3-O-glucoside (Isoquercetrin) Extrasynthese, France Quercetin-3-O-rhamnoside (Quercitrin) Extrasynthese, France Quercetin-3-O-rutinoside (Rutin) Extrasynthese, France Quercetin-4′-O-glucoside (Spiraeoside) Sigma Aldrich, USA Tiliroside Extrasynthese, France Quercetin-d3 Toronto Research Chemicals, CAN Flavones 5,7-Dimethoxyflavone Sigma Aldrich, USA Apigenin Extrasynthese, France Apigenin-7-O-glucoside Extrasynthese, France Apigenin-7-O-neohesperidoside Extrasynthese, France Apigenin-7-O-rutinoside Extrasynthese, France Apigenin-8-C-glucoside (Vitexin) Extrasynthese, France Chrysin Extrasynthese, France Diosmetin Sigma Aldrich, USA Diosmetin-7-O-rutinoside Sigma Aldrich, USA Flavone Sigma Aldrich, USA Luteolin Extrasynthese, France Luteolin-3',7-di-O-glucoside Extrasynthese, France Luteolin-4'-O-glucoside Extrasynthese, France Luteolin-7-O-glucoside Extrasynthese, France Luteolin-7-O-rutinoside Sigma Aldrich, USA Luteolin-8'-C-glucoside Extrasynthese, France Tricetin Extrasynthese, France Tangeretin Extrasynthese, France Vitexin-2'-O-rhamnoside Extrasynthese, France Flavan-3-ols (+)-Catechin Extrasynthese, France (-)-catechin gallate Extrasynthese, France Supporting Information for Publication (-)-Epicatechin Extrasynthese, France (-)-Epicatechin gallate Extrasynthese, France (-)-Epigallocatechin Extrasynthese, France (-)-Epigallocatechin gallate Extrasynthese, France (-)-Gallocatechin Sigma Aldrich, USA ±-Catechin-2,3,4-13C3 Sigma Aldrich, USA Flavanones Eriocitrin Extrasynthese, France Eriodictyol Extrasynthese, France Flavanone Sigma Aldrich, USA Hesperetin Sigma Aldrich, USA Hesperetin-7-O-rutinoside Sigma Aldrich, USA Isosakuranetin Extrasynthese, France Narigenin-7-O-rutinoside Sigma Aldrich, USA Naringenin Sigma Aldrich, USA Dihydroflavonols Dihydromyricetin Sigma Aldrich, USA Dihydrokaempferol Sigma Aldrich, USA Taxifolin (dihydroquercetin) Sigma Aldrich, USA Stilbenes Resveratrol Sigma Aldrich, USA Resveratrol-3-β-mono-D-glucoside (Polydatin) Santa Cruz Biotech, USA Resveratrol-(4-hydroxyphenyl-13C6) Sigma Aldrich, USA Hydroxybenzoic acids 3,4-Dihydroxybenzoic acid Sigma Aldrich, USA 4-amino salicylic acid Sigma Aldrich, USA 4-hydroxybenzoic acid Sigma Aldrich, USA Gallic acid Sigma Aldrich, USA Salicin Sigma Aldrich, USA Syringic acid Extrasynthese, France Vanillic acid Sigma Aldrich, USA Vanillic acid-4-β-D-glucoside Sigma Aldrich, USA Vanillin Sigma Aldrich, USA Vanillin-(ring-13C6) Sigma Aldrich, USA 4-hydroxybenzoic acid - 13C7 Sigma Aldrich, USA Hydroxycinnamic acids Caffeic acid Sigma Aldrich, USA Supporting Information for Publication Chlorogenic acid Sigma Aldrich, USA Ferulic acid (trans) Sigma Aldrich, USA p-Coumaric acid (trans) Sigma Aldrich, USA trans-3-hydroxycinnamic acid Sigma Aldrich, USA Ferulic acid-D3 Toronto Research Chemicals, CAN Isoflavones Genistein Sigma Aldrich, USA Prunetin Sigma Aldrich, USA Procyanidins Procyanidin A2 Sigma Aldrich, USA Procyanidin B1 Sigma Aldrich, USA Procyanidin B2 Sigma Aldrich, USA Procyanidin B3 AdooQ, USA Procyanidin C1 Sigma Aldrich, USA Supporting Information for Publication Table S2. Identification of the upregulated compounds in each seed coat group and/or shared with other groups (from the volcano plots in Figure 2 & 5. Identification levels are: confirmed (1), putative (2), isomeric (2/3), class only (3) and unidentified (4). Name Formula Calculated Molecular Weight RT [min] Mass error (ppm) Identification level Black/black (not significantly upregulated in dark green/marbled nor green/dotted) seed coats Gallic acid isomer C7 H6 O5 170.02086 4.22 -3.91 2/3 Gallocatechin hexoside C21 H24 O12 468.12703 8.07 0.54 2/3 Myricetin hexoside feruloyl hexoside C33 H38 O24 818.17751 8.23 2.70 2/3 Prodelphinidin dimer (GG) C30 H26 O14 610.13321 9.10 1.57 2/3 Prodelphinidin derivative/adduct C41 H40 O25 932.18812 9.99 2.42 3 Apigenin C-hexoside C-pentoside C26 H28 O14 564.14917 11.26 2.24 2/3 Apigenin C-hexoside C-pentoside C26 H28 O14 564.14913 11.39 2.18 2/3 Tricetin di-hexoside C27 H30 O17 626.14967 14.58 2.18 2/3 Methoxy-tetrahydroxy-flavone hexoside C22 H22 O12 478.11169 16.39 1.18 2/3 Dark green/marbled (not significantly upregulated in green/dotted nor black/black) seed coats Leucinic acid hexoside C12 H22 O8 294.13182 4.99 1.19 2/3 Unknown hexoside C13 H24 O8 308.14773 7.13 1.98 3 Luteolin deoxyhexoside di-pentoside C30 H32 O19 696.15593 14.06 3.10 2/3 Supporting Information for Publication Green/dotted (not significantly upregulated in dark green/marbled nor black/black) seed coats Dihydroxybenzoic acid hexoside C13 H16 O9 316.07983 8.78 1.24 2/3 Dihydroxybenzoic acid malonyl hexoside C16 H18 O12 402.08069 12.69 2.15 2/3 Tricetin hexoside malonyl hexoside C30 H32 O20 712.14986 16.36 1.63 2/3 Unknown acetyl hexoside C23 H24 O11 476.1326 19.60 1.54 3 Black/black and dark green/marbled (not significantly upregulated in green/dotted) seed coats Unidentified 582.15974 9.76 4 Jasmonic acid derivative C20 H34 O11 450.21095 11.05 1.87 3 Heliotropic acid gallate C15 H10 O8 318.03813 15.67 1.77 2/3 Methoxy-tetrahydroxy-flavone hexoside C22 H22 O12 478.11174 16.93 1.28 2/3 Methoxy-tetrahydroxy-flavone C16 H12 O7 316.05892 19.28 1.94 2/3 Black/black and green/dotted (not significantly upregulated in dark green/marbled) seed coats Delphinidin derivative C32 H40 O22 776.20224 7.22 1.43 3 Methoxy-tetrahydroxy-flavone malonyl hexoside C25 H24 O15 564.11265 17.65 2.00 2/3 Dark green/marbled and green/dotted (not significantly upregulated in black/black) seed coats Tricetin hexoside malonyl hexoside C30 H32 O20 712.15086 14.64 3.04 2/3 Tricetin malonyl hexoside C24 H22 O15 550.09704 15.31 2.13 2/3 Luteolin malonyl hexoside C24 H22 O14 534.10193 16.63 1.83 2/3 Luteolin malonyl hexoside C24 H22 O14 534.10192 18.13 1.80 2/3 Luteolin malonyl hexoside C24 H22 O14 534.10189 18.58 1.75 2/3 Supporting Information for Publication 8 10/20 eV 50/60 eV 10. Delphinidin 3-O-(2-O-β-d- Glucopyranosyl-α-l-arabinopyranoside) C26H28O16 596.1389 6.71 1.92 2 Supporting Information for Publication 9 11. Phenolic acid pentoside derivative C20H24O14 488.1172 7.22 1.20 3 10/20 eV 50/60 eV Supporting Information for Publication 10 12. Phenolic acid derivative C29H34O17 654.1816 7.60 3.00 3 10/20 eV 50/60 eV Supporting Information for Publication 11 13. Delphinidin derivative C29H34O17 654.1811 9.79 2.36 3 10/20 eV 50/60 eV Supporting Information for Publication 12 14. Delphinidin derivative C29H34O17 654.1811 10.26 2.36 3 10/20 eV 10/20 eV Supporting Information for Publication 13 15. Dihydroxy methoxy benzoic acid gallate C15H12O9 336.0488 10.43 2.02 2/3 10/20 eV 50/60 eV Supporting Information for Publication 14 16. Dimethoxy hydroxybenzoic acid gallate C16H14O9 350.0645 12.10 1.94 2/3 10/20 eV 50/60 eV Supporting Information for Publication 15 17. Hydroxy-tricetin hexoside pentoside C26H28O17 612.1342 12.68 2.47 2/3 10/20 eV 50/60 eV Supporting Information for Publication 16 18. Gallic acid pentoside hexoside C21H20O12 464.0961 12.87 1.26 2/3 10/20 eV 50/60 eV Supporting Information for Publication 17 19. Tricetin pentoside C20H18O11 434.0857 13.53 1.86 2/3 10/20 eV 50/60 eV Supporting Information for Publication 18 50/60 eV (zoomed-in) Supporting Information for Publication 19 20. Luteolin hexoside C21H20O11 448.1009 14.36 0.85 2/3 10/20 eV 50/60 eV Supporting Information for Publication 20 21. Tricetin hexoside malonyl hexoside C30H32O20 712.1509 14.64 3.04 2/3 10/20 eV 50/60 eV Supporting Information for Publication 21 50/60 eV (zoomed-in) Supporting Information for Publication 22 22. Tricetin pentoside malonyl hexoside C29H30O19 682.1397 15.07 2.25 2/3 10/20 eV 50/60 eV Supporting Information for Publication 23 50/60 eV (zoomed-in) Supporting Information for Publication 24 23. Luteolin pentoside C20H18O10 418.0910 15.12 2.31 2/3 10/20 eV 50/60 eV Supporting Information for Publication 25 24. Tricetin malonyl hexoside isomer C24H22O15 550.0970 15.31 2.13 2/3 10/20 eV 50/60 eV Supporting Information for Publication 26 50/60 eV (zoomed-in) Supporting Information for Publication 27 25. Tricetin hexoside C21H20O12 464.0961 15.42 1.23 2/3 10/20 eV 50/60 eV Supporting Information for Publication 28 50/60 eV (zoomed-in) Supporting Information for Publication 29 27. Luteolin 4’-O-glucoside C21H20O11 448.1010 16.37 0.93 1 10/20 eV 50/60 eV Supporting Information for Publication 30 28. Luteolin malonyl hexoside C24H22O14 534.1019 16.63 1.83 2/3 10/20 eV 50/60 eV Supporting Information for Publication 31 29. Tricetin malonyl hexoside C24H22O15 550.0970 16.78 2.12 2/3 10/20 eV 50/60 eV Supporting Information for Publication 32 30. Luteolin hexoside C21H20O11 448.1009 16.89 0.84 2/3 10/20 eV 50/60 eV Supporting Information for Publication 33 31. Tricetin hexoside C21H20O12 464.0960 17.01 1.18 2/3 10/20 eV 50/60 eV Supporting Information for Publication 34 32. Tricetin C15H10O7 302.0428 17.50 0.43 1 10/20 eV 50/60 eV Supporting Information for Publication 35 33. Tricetin acetyl hexoside C23H22O13 506.1067 17.86 1.29 2/3 10/20 eV 50/60 eV Supporting Information for Publication 36 50/60 eV (zoomed-in) Supporting Information for Publication 37 34. Luteolin malonyl hexoside C24H22O14 534.1019 18.13 1.80 2/3 10/20 eV 50/60 eV Supporting Information for Publication 38 35. Luteolin malonyl hexoside C24H22O14 534.1019 18.58 1.75 2/3 10/20 eV 50/60 eV Supporting Information for Publication 39 36. Tricetin malonyl hexoside C24H22O15 550.0970 19.07 1.99 2/3 10/20 eV 50/60 eV Supporting Information for Publication 40 37. Luteolin C15H10O6 286.0478 19.47 0.33 1 10/20 eV 50/60 eV Figure S1. Full scan and MS/MS spectra of the putatively identified metabolites in Table 2. Supporting Information for Publication 41 Compounds written in red are upregulated in the volcano plots for green/patterned and black/black seed coats versus green/absent seed coats (23 compounds). Supporting Information for Publication 42 Summary S1. Parameters used in generating the analysis of patterned lentil seed coat samples using the Compound Discoverer software. Workflow Search name: PatternedSeedCoats_19Mar2022_CD3.2_NormNone_QC- RSD50_MaxCandidates50_ShiftRefFalse_16DB_MinPeak6M_30-40eV Search description: Untargeted Metabolomics workflow: Find and identify the differences between samples. - Performs retention time alignment, unknown compound detection, and compound grouping across all samples. Predicts elemental compositions for all compounds, fills gaps across all samples, and hides chemical background (using Blank samples). Identifies compounds using mzCloud (ddMS2) and ChemSpider (formula or exact mass). Also performs similarity search for all compounds with ddMS2 data using mzCloud. Applies mzLogic algorithm to rank order ChemSpider results. Maps compounds to biological pathways using Metabolika. Applies QC-based batch normalization if QC samples are available. Calculates differential analysis (t-test or ANOVA), determines p-values, adjusted p-values, ratios, fold change, CV, etc.). Search date: 3/19/2022 9:02:04 PM Created with Discoverer version: 3.2.0.421 [Input Files (6)] -->Select Spectra (33) [Select Spectra (33)] -->Align Retention Times (26) [Align Retention Times (26)] -->Detect Compounds (9) [Detect Compounds (9)] -->Group Compounds (31) [Group Compounds (31)] -->Fill Gaps (32) -->Search ChemSpider (23) Supporting Information for Publication 43 -->Map to Metabolika Pathways (34) -->Search Mass Lists (36) -->Predict Compositions (29) -->Assign Compound Annotations (25) -->Search mzCloud (22) -->Search mzVault (37) [Fill Gaps (32)] -->Apply QC Correction (43) [Apply QC Correction (43)] -->Mark Background Compounds (40) [Search ChemSpider (23)] -->Apply mzLogic (35) [Map to Metabolika Pathways (34)] -->Apply mzLogic (35) [Search Mass Lists (36)] -->Apply mzLogic (35) [Mark Background Compounds (40)] [Apply mzLogic (35)] [Predict Compositions (29)] [Assign Compound Annotations (25)] [Search mzCloud (22)] Supporting Information for Publication 44 [Search mzVault (37)] [Differential Analysis (17)] [Descriptive Statistics (38)] ------------------------------------------------------------------ Processing node 6: Input Files ------------------------------------------------------------------ Input Data: - File Name(s) (Hidden): E:\QE Data\2019Jan18\190118QE_001.raw E:\QE Data\2019Jan18\190118QE_002.raw E:\QE Data\2019Jan18\190118QE_004.raw E:\QE Data\2019Jan18\190118QE_005.raw E:\QE Data\2019Jan18\190118QE_006.raw E:\QE Data\2019Jan18\190118QE_007.raw E:\QE Data\2019Jan18\190118QE_008.raw E:\QE Data\2019Jan18\190118QE_009.raw E:\QE Data\2019Jan18\190118QE_010.raw E:\QE Data\2019Jan18\190118QE_011.raw E:\QE Data\2019Jan18\190118QE_012.raw E:\QE Data\2019Jan18\190118QE_013.raw E:\QE Data\2019Jan18\190118QE_014.raw E:\QE Data\2019Jan18\190118QE_015.raw E:\QE Data\2019Jan18\190118QE_016.raw E:\QE Data\2019Jan18\190118QE_017.raw E:\QE Data\2019Jan18\190118QE_019.raw E:\QE Data\2019Jan18\190118QE_021.raw E:\QE Data\2019Jan18\190118QE_022.raw E:\QE Data\2019Jan18\190118QE_023.raw Supporting Information for Publication 45 E:\QE Data\2019Jan18\190118QE_024.raw E:\QE Data\2019Jan18\190118QE_026.raw E:\QE Data\2019Jan18\190118QE_027.raw E:\QE Data\2019Jan18\190118QE_028.raw E:\QE Data\2019Jan18\190118QE_029.raw E:\QE Data\2019Jan18\190118QE_031.raw E:\QE Data\2019Jan18\190118QE_033.raw E:\QE Data\2019Jan18\190118QE_035.raw E:\QE Data\2019Jan18\190118QE_037.raw E:\QE Data\2019Jan18\190118QE_038.raw E:\QE Data\2019Jan18\190118QE_039.raw E:\QE Data\2019Jan18\190118QE_040.raw E:\QE Data\2019Jan18\190118QE_041.raw E:\QE Data\2019Jan18\190118QE_042.raw E:\QE Data\2019Jan18\190118QE_043.raw E:\QE Data\2019Jan18\190118QE_044.raw E:\QE Data\2019Jan18\190118QE_045.raw E:\QE Data\2019Jan18\190118QE_047.raw E:\QE Data\2019Jan18\190118QE_049.raw E:\QE Data\2019Jan18\190118QE_050.raw E:\QE Data\2019Jan18\190118QE_051.raw E:\QE Data\2019Jan18\190118QE_053.raw E:\QE Data\2019Jan18\190118QE_054.raw E:\QE Data\2019Jan18\190118QE_055.raw E:\QE Data\2019Jan18\190118QE_056.raw E:\QE Data\2019Jan18\190118QE_057.raw E:\QE Data\2019Jan18\190118QE_058.raw E:\QE Data\2019Jan18\190118QE_060.raw E:\QE Data\2019Jan18\190118QE_061.raw E:\QE Data\2019Jan18\190118QE_063.raw E:\QE Data\2019Jan18\190118QE_065.raw Supporting Information for Publication 46 E:\QE Data\2019Jan18\190118QE_066.raw E:\QE Data\2019Jan18\190118QE_067.raw E:\QE Data\2019Jan18\190118QE_068.raw E:\QE Data\2019Jan18\190118QE_069.raw E:\QE Data\2019Jan18\190118QE_070.raw E:\QE Data\2019Jan18\190118QE_071.raw E:\QE Data\2019Jan18\190118QE_072.raw E:\QE Data\2019Jan18\190118QE_074.raw E:\QE Data\2019Jan18\190118QE_076.raw E:\QE Data\2019Jan18\190118QE_077.raw E:\QE Data\2019Jan18\190118QE_078.raw E:\QE Data\2019Jan18\190118QE_079.raw E:\QE Data\2019Jan18\190118QE_081.raw E:\QE Data\2019Jan18\190118QE_082.raw E:\QE Data\2019Jan18\190118QE_083.raw E:\QE Data\2019Jan18\190118QE_084.raw E:\QE Data\2019Jan18\190118QE_085.raw E:\QE Data\2019Jan18\190118QE_086.raw E:\QE Data\2019Jan18\190118QE_090.raw E:\QE Data\2019Jan18\190118QE_092.raw E:\QE Data\2019Jan18\190118QE_094.raw E:\QE Data\2019Jan18\190118QE_095.raw E:\QE Data\2019Jan18\190118QE_096.raw E:\QE Data\2019Jan18\190118QE_097.raw E:\QE Data\2019Jan18\190118QE_098.raw E:\QE Data\2019Jan18\190118QE_100.raw ------------------------------------------------------------------ Processing node 33: Select Spectra ------------------------------------------------------------------ 1. Spectrum Properties Filter: - Lower RT Limit: 1.2 Supporting Information for Publication 47 - Upper RT Limit: 25 - First Scan: 0 - Last Scan: 0 - Ignore Specified Scans: (not specified) - Lowest Charge State: 0 - Highest Charge State: 3 - Min. Precursor Mass: 140 Da - Max. Precursor Mass: 4000 Da - Total Intensity Threshold: 0 - Minimum Peak Count: 1 2. Scan Event Filters: - Mass Analyzer: (not specified) - MS Order: Any - Activation Type: (not specified) - Min. Collision Energy: 0 - Max. Collision Energy: 1000 - Scan Type: Any - Polarity Mode: Any 3. Peak Filters: - S/N Threshold (FT-only): 1.5 4. Replacements for Unrecognized Properties: - Unrecognized Charge Replacements: 1 - Unrecognized Mass Analyzer Replacements: ITMS - Unrecognized MS Order Replacements: MS2 - Unrecognized Activation Type Replacements: CID - Unrecognized Polarity Replacements: + - Unrecognized MS Resolution@200 Replacements: 60000 - Unrecognized MSn Resolution@200 Replacements: 30000 Supporting Information for Publication 48 5. General Settings: - Precursor Selection: Use MS1 Precursor - Use Isotope Pattern in Precursor Reevaluation: True - Provide Profile Spectra: Automatic - Store Chromatograms: False ------------------------------------------------------------------ Processing node 26: Align Retention Times ------------------------------------------------------------------ 1. General Settings: - Alignment Model: Adaptive curve - Alignment Fallback: Use Linear Model - Maximum Shift [min]: 2 - Shift Reference File: False - Mass Tolerance: 5 ppm - Remove Outlier: True ------------------------------------------------------------------ Processing node 9: Detect Compounds ------------------------------------------------------------------ 1. General Settings: - Mass Tolerance [ppm]: 5 ppm - Intensity Tolerance [%]: 30 - S/N Threshold: 3 - Min. Peak Intensity: 6000000 - Ions: [2M+FA-H]-1 [2M-H]-1 [M+FA-H]-1 [M-2H]-2 [M-H]-1 [M-H-H2O]-1 Supporting Information for Publication 49 - Base Ions: [M-H]-1 - Min. Element Counts: C H O - Max. Element Counts: C150 H300 N10 Na2 O150 P S2 2. Peak Detection: - Filter Peaks: True - Max. Peak Width [min]: 0.5 - Remove Singlets: True - Min. # Scans per Peak: 10 - Min. # Isotopes: 1 3. Isotope Grouping: - Min. Spectral Distance Score: 0 - Remove Potentially False Positive Isotopes: True ------------------------------------------------------------------ Processing node 31: Group Compounds ------------------------------------------------------------------ 1. Compound Consolidation: - Mass Tolerance: 5 ppm - RT Tolerance [min]: 0.2 2. Fragment Data Selection: - Preferred Ions: [M-2H]-2; [M-H]-1 ------------------------------------------------------------------ Processing node 32: Fill Gaps ------------------------------------------------------------------ 1. General Settings: - Mass Tolerance: 5 ppm Supporting Information for Publication 50 - S/N Threshold: 1.5 - Use Real Peak Detection: True ------------------------------------------------------------------ Processing node 43: Apply QC Correction ------------------------------------------------------------------ 1. General Settings: - Regression Model: Linear - Min. QC Coverage [%]: 75 - Max. QC Area RSD [%]: 30 - Max. Corrected QC Area RSD [%]: 25 - Max. # Files Between QC Files: 10 ------------------------------------------------------------------ Processing node 40: Mark Background Compounds ------------------------------------------------------------------ 1. General Settings: - Max. Sample/Blank: 5 - Max. Blank/Sample: 0 - Hide Background: True ------------------------------------------------------------------ Processing node 23: Search ChemSpider ------------------------------------------------------------------ 1. Search Settings: - Database(s): BioCyc Carotenoids Database Cayman Chemical ChEBI ChEMBL FooDB Human Metabolome Database KEGG Supporting Information for Publication 51 MassBank NIST Phenol-Explorer PlantCyc Royal Society of Chemistry Sigma-Aldrich SMPDB Small Molecule Pathway Database The Merck Index Online - Search Mode: By Formula or Mass - Mass Tolerance: 5 ppm - Max. # of results per compound: 100 - Max. # of Predicted Compositions to be searched per Compound: 3 - Result Order (for Max. # of results per compound): Order By Reference Count (DESC) 2. Predicted Composition Annotation: - Check All Predicted Compositions: False ------------------------------------------------------------------ Processing node 35: Apply mzLogic ------------------------------------------------------------------ 1. Search Settings: - FT Fragment Mass Tolerance: 10 ppm - IT Fragment Mass Tolerance: 0.4 Da - Max. # Compounds: 10 - Max. # mzCloud Similarity Results to consider per Compound: 10 - Match Factor Threshold: 30 ------------------------------------------------------------------ Processing node 34: Map to Metabolika Pathways ------------------------------------------------------------------ 1. Search Settings: - Metabolika Pathways: (3R)-linalool biosynthesis.metabolika|2-nitrobenzoate degradation I.metabolika|2-oxobutanoate degradation I.metabolika|3-phenylpropanoate and 3-(3- hydroxyphenyl)propanoate degradation.metabolika|3-phenylpropanoate degradation.metabolika|Acetyl- Supporting Information for Publication 52 CoA fermentation to butanoate II.metabolika|Adenosylcobalamin biosynthesis I (anaerobic).metabolika|Adenosylcobalamin biosynthesis II (aerobic).metabolika|Allantoin degradation IV (anaerobic).metabolika|Allantoin degradation to glyoxylate I.metabolika|Allantoin degradation to glyoxylate II.metabolika|Allantoin degradation to glyoxylate III.metabolika|Ammonia assimilation cycle I.metabolika|Ammonia assimilation cycle III.metabolika|Ammonia oxidation IV (autotrophic ammonia oxidizers).metabolika|Anaerobic aromatic compound degradation (Thauera aromatica).metabolika|Anaerobic energy metabolism (invertebrates, mitochondrial).metabolika|Arachidonate biosynthesis III (6-desaturase, mammals).metabolika|Archaetidylinositol biosynthesis.metabolika|Archaetidylserine and archaetidylethanolamine biosynthesis.metabolika|Arginine, ornithine and proline interconversion.metabolika|Aromatic compounds degradation via ss-ketoadipate.metabolika|Aspartate superpathway.metabolika|B-carotene biosynthesis (engineered).metabolika|Bacillibactin biosynthesis.metabolika|Benzoate biosynthesis I (CoA-dependent, ss-oxidative).metabolika|Benzoate biosynthesis III (CoA-dependent, non-ss-oxidative).metabolika|Benzoate fermentation (to acetate and cyclohexane carboxylate).metabolika|Biotin biosynthesis I.metabolika|Biotin biosynthesis II.metabolika|Bitter acids biosynthesis.metabolika|Caffeine degradation IV (bacteria, via demethylation and oxidation).metabolika|Cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas).metabolika|Catechol degradation I (meta-cleavage pathway).metabolika|Catechol degradation II (meta-cleavage pathway).metabolika|Catechol degradation III (ortho-cleavage pathway).metabolika|Cellulose and hemicellulose degradation (cellulolosome).metabolika|Chitin biosynthesis.metabolika|Cholesterol biosynthesis I.metabolika|Cholesterol biosynthesis II (via 24,25- dihydrolanosterol).metabolika|Cholesterol biosynthesis III (via desmosterol).metabolika|Choline degradation IV.metabolika|Choline-O-sulfate degradation.metabolika|Chondroitin sulfate biosynthesis.metabolika|Chorismate biosynthesis I.metabolika|Chorismate biosynthesis II (archaea).metabolika|Colanic acid building blocks biosynthesis.metabolika|Crotonate fermentation (to acetate and cyclohexane carboxylate).metabolika|Curcuminoid biosynthesis.metabolika|D-serine metabolism.metabolika|Dermatan sulfate biosynthesis.metabolika|Enterobacterial common antigen biosynthesis.metabolika|Enterobactin biosynthesis.metabolika|G-butyrobetaine degradation.metabolika|GABA shunt.metabolika|Gamma-glutamyl cycle.metabolika|Gluconeogenesis II (Methanobacterium thermoautotrophicum).metabolika|Glycerol and glycerophosphodiester degradation.metabolika|Glycerol degradation to butanol.metabolika|Glycine biosynthesis II.metabolika|Heparan sulfate biosynthesis.metabolika|Hexitol fermentation to lactate, formate, ethanol and acetate.metabolika|Homolactic fermentation.metabolika|Hyperxanthone E biosynthesis.metabolika|Icosapentaenoate biosynthesis III (fungi).metabolika|Icosapentaenoate biosynthesis IV (bacteria).metabolika|Isoprene biosynthesis I.metabolika|Kanamycin biosynthesis.metabolika|Kauralexin biosynthesis.metabolika|Kdo transfer to lipid IVA III (Chlamydia).metabolika|Ketogluconate metabolism.metabolika|L-alanine fermentation to propanoate and acetate.metabolika|L-arginine biosynthesis I (via L-ornithine).metabolika|L-arginine degradation V (arginine deiminase pathway).metabolika|L-ascorbate biosynthesis V.metabolika|L-cysteine biosynthesis IV (from L-methionine).metabolika|L-cysteine biosynthesis IV (fungi).metabolika|L-glutamate and L- glutamine biosynthesis.metabolika|L-glutamate degradation IX (via 4-aminobutanoate).metabolika|L- glutamate degradation VII (to butanoate).metabolika|L-glutamate degradation VIII (to propanoate).metabolika|L-homoserine and L-methionine biosynthesis.metabolika|L-methionine biosynthesis III.metabolika|L-methionine salvage cycle I (bacteria and plants).metabolika|L-methionine salvage cycle II (plants).metabolika|L-methionine salvage cycle III.metabolika|L-tryptophan degradation III (eukaryotic).metabolika|L-tryptophan degradation IX.metabolika|L-tryptophan degradation XI (mammalian, via kynurenine).metabolika|L-tryptophan degradation XII (Geobacillus).metabolika|L- tyrosine degradation IV (to 4-methylphenol).metabolika|Mandelate degradation to acetyl- CoA.metabolika|Meta cleavage pathway of aromatic compounds.metabolika|Methanobacterium thermoautotrophicum biosynthetic metabolism.metabolika|Methanol and methylamine oxidation to formaldehyde.metabolika|Methanol oxidation to carbon dioxide.metabolika|Methylglyoxal degradation Supporting Information for Publication 53 IV.metabolika|MRNA capping II.metabolika|Myo-, chiro- and scillo-inositol degradation.metabolika|N- acetylglucosamine degradation II.metabolika|NAD biosynthesis II (from tryptophan).metabolika|NAD salvage pathway III.metabolika|Naphthalene degradation to acetyl-CoA.metabolika|Nitrifier denitrification.metabolika|Novobiocin biosynthesis.metabolika|O-antigen building blocks biosynthesis (E. coli).metabolika|Oxygenic photosynthesis.metabolika|P-cumate degradation.metabolika|P-cymene degradation.metabolika|Pentose phosphate pathway.metabolika|Peptidoglycan biosynthesis I (meso- diaminopimelate containing).metabolika|Peptidoglycan biosynthesis II (staphylococci).metabolika|Peptidoglycan biosynthesis III (mycobacteria).metabolika|Peptidoglycan biosynthesis IV (Enterococcus faecium).metabolika|Peptidoglycan biosynthesis V (ss-lactam resistance).metabolika|Phosphatidylglycerol biosynthesis I (plastidic).metabolika|Phosphatidylglycerol biosynthesis II (non-plastidic).metabolika|Plant sterol biosynthesis.metabolika|Polyisoprenoid biosynthesis (E. coli).metabolika|Purine nucleotides degradation I (plants).metabolika|Purine nucleotides degradation II (aerobic).metabolika|Pyrimidine nucleobases salvage II.metabolika|Pyruvate fermentation to acetate and alanine.metabolika|Pyruvate fermentation to acetate and lactate I.metabolika|Pyruvate fermentation to acetate and lactate II.metabolika|Pyruvate fermentation to acetate I.metabolika|Pyruvate fermentation to acetate III.metabolika|Pyruvate fermentation to acetate IV.metabolika|Pyruvate fermentation to acetate V.metabolika|Pyruvate fermentation to acetate VI.metabolika|Pyruvate fermentation to acetate VII.metabolika|Reactive oxygen species degradation.metabolika|S-adenosyl-L- methionine cycle I.metabolika|Salicylate glucosides biosynthesis I.metabolika|Sphingolipid biosynthesis (mammals).metabolika|Sucrose biosynthesis I (from photosynthesis).metabolika|Sulfate reduction I (assimilatory).metabolika|Superpathway avenacin A biosynthesis.metabolika|Superpathway NADNADP - NADHNADPH interconversion (yeast).metabolika|Superpathway of (Kdo)2-lipid A biosynthesis.metabolika|Superpathway of (R,R)-butanediol biosynthesis.metabolika|Superpathway of 1D- myo-inositol hexakisphosphate biosynthesis (plants).metabolika|Superpathway of 2,3-butanediol biosynthesis.metabolika|Superpathway of 4-aminobutanoate degradation.metabolika|Superpathway of 4- hydroxybenzoate biosynthesis (yeast).metabolika|Superpathway of 5-aminoimidazole ribonucleotide biosynthesis.metabolika|Superpathway of acetate utilization and formation.metabolika|Superpathway of acetyl-CoA biosynthesis.metabolika|Superpathway of acrylonitrile degradation.metabolika|Superpathway of adenosine nucleotides de novo biosynthesis I.metabolika|Superpathway of adenosine nucleotides de novo biosynthesis II.metabolika|Superpathway of aerobic toluene degradation.metabolika|Superpathway of aflatoxin biosynthesis.metabolika|Superpathway of allantoin degradation in plants.metabolika|Superpathway of allantoin degradation in yeast.metabolika|Superpathway of Allium flavor precursors.metabolika|Superpathway of ammonia assimilation (plants).metabolika|Superpathway of anaerobic energy metabolism (invertebrates).metabolika|Superpathway of anaerobic sucrose degradation.metabolika|Superpathway of anthocyanin biosynthesis (from cyanidin and cyanidin 3-O- glucoside).metabolika|Superpathway of anthocyanin biosynthesis (from delphinidin 3-O- glucoside).metabolika|Superpathway of anthocyanin biosynthesis (from pelargonidin 3-O- glucoside).metabolika|Superpathway of arginine and polyamine biosynthesis.metabolika|Superpathway of aromatic amino acid biosynthesis.metabolika|Superpathway of aromatic compound degradation via 2- oxopent-4-enoate.metabolika|Superpathway of aromatic compound degradation via 3- oxoadipate.metabolika|Superpathway of atrazine degradation.metabolika|Superpathway of bacteriochlorophyll a biosynthesis.metabolika|Superpathway of benzoxazinoid glucosides biosynthesis.metabolika|Superpathway of betalain biosynthesis.metabolika|Superpathway of branched chain amino acid biosynthesis.metabolika|Superpathway of butirocin biosynthesis.metabolika|Superpathway of C1 compounds oxidation to CO2.metabolika|Superpathway of C28 brassinosteroid biosynthesis.metabolika|Superpathway of candicidin biosynthesis.metabolika|Superpathway of carotenoid biosynthesis.metabolika|Superpathway of CDP- glucose-derived O-antigen building blocks biosynthesis.metabolika|Superpathway of cholesterol biosynthesis.metabolika|Superpathway of cholesterol degradation I (cholesterol oxidase).metabolika|Superpathway of cholesterol degradation II (cholesterol dehydrogenase).metabolika|Superpathway of choline biosynthesis.metabolika|Superpathway of Supporting Information for Publication 54 chorismate metabolism.metabolika|Superpathway of CMP-sialic acids biosynthesis.metabolika|Superpathway of coenzyme A biosynthesis I.metabolika|Superpathway of coenzyme A biosynthesis II (plants).metabolika|Superpathway of coenzyme A biosynthesis III (mammals).metabolika|Superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle.metabolika|Superpathway of D-glucarate and D-galactarate degradation.metabolika|Superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism.metabolika|Superpathway of demethylmenaquinol-6 biosynthesis I.metabolika|Superpathway of demethylmenaquinol-6 biosynthesis II.metabolika|Superpathway of demethylmenaquinol-8 biosynthesis.metabolika|Superpathway of demethylmenaquinol-9 biosynthesis.metabolika|Superpathway of dimethylsulfone degradation.metabolika|Superpathway of dimethylsulfoniopropanoate degradation.metabolika|Superpathway of diterpene resin acids biosynthesis.metabolika|Superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis.metabolika|Superpathway of dTDP- glucose-derived O-antigen building blocks biosynthesis.metabolika|Superpathway of ergosterol biosynthesis I.metabolika|Superpathway of ergosterol biosynthesis II.metabolika|Superpathway of ergotamine biosynthesis.metabolika|Superpathway of erythromycin biosynthesis (without sugar biosynthesis).metabolika|Superpathway of erythromycin biosynthesis.metabolika|Superpathway of fatty acid biosynthesis I (E. coli).metabolika|Superpathway of fatty acid biosynthesis II (plant).metabolika|Superpathway of fatty acid biosynthesis initiation (E. coli).metabolika|Superpathway of fatty acids biosynthesis (E. coli).metabolika|Superpathway of fermentation (Chlamydomonas reinhardtii).metabolika|Superpathway of flavones and derivatives biosynthesis .metabolika|Superpathway of formononetin derivative biosynthesis.metabolika|Superpathway of fucose and rhamnose degradation.metabolika|Superpathway of fumitremorgin biosynthesis.metabolika|Superpathway of GDP- mannose-derived O-antigen building blocks biosynthesis.metabolika|Superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP).metabolika|Superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate).metabolika|Superpathway of gibberellin biosynthesis.metabolika|Superpathway of gibberellin GA12 biosynthesis.metabolika|Superpathway of glucose and xylose degradation.metabolika|Superpathway of glycerol degradation to 1,3- propanediol.metabolika|Superpathway of glycol metabolism and degradation.metabolika|Superpathway of glycolysis and Entner-Doudoroff.metabolika|Superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass.metabolika|Superpathway of glyoxylate bypass and TCA.metabolika|Superpathway of glyoxylate cycle and fatty acid degradation.metabolika|Superpathway of guanine and guanosine salvage.metabolika|Superpathway of guanosine nucleotides degradation (plants).metabolika|Superpathway of guanosine nucleotides de novo biosynthesis I.metabolika|Superpathway of guanosine nucleotides de novo biosynthesis II.metabolika|Superpathway of heme biosynthesis from glutamate.metabolika|Superpathway of heme biosynthesis from glycine.metabolika|Superpathway of heme biosynthesis from uroporphyrinogen- III.metabolika|Superpathway of hexitol degradation (bacteria).metabolika|Superpathway of hexuronide and hexuronate degradation.metabolika|Superpathway of histidine, purine, and pyrimidine biosynthesis.metabolika|Superpathway of hydrogen production.metabolika|Superpathway of hydrolyzable tannin biosynthesis.metabolika|Superpathway of hyoscyamine and scopolamine biosynthesis.metabolika|Superpathway of indole-3-acetate conjugate biosynthesis.metabolika|Superpathway of inositol phosphate compounds.metabolika|Superpathway of isoflavonoids (via naringenin).metabolika|Superpathway of jasmonoyl-amino acid conjugates biosynthesis.metabolika|Superpathway of L-alanine biosynthesis.metabolika|Superpathway of L-arginine and L-ornithine degradation.metabolika|Superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation.metabolika|Superpathway of L-asparagine biosynthesis.metabolika|Superpathway of L- aspartate and L-asparagine biosynthesis.metabolika|Superpathway of L-citrulline metabolism.metabolika|Superpathway of L-cysteine biosynthesis (mammalian).metabolika|Superpathway of L-isoleucine biosynthesis I.metabolika|Superpathway of L-lysine degradation.metabolika|Superpathway of L-lysine, L-threonine and L-methionine biosynthesis I.metabolika|Superpathway of L-lysine, L-threonine and L-methionine biosynthesis Supporting Information for Publication 55 II.metabolika|Superpathway of L-methionine biosynthesis (by sulfhydrylation).metabolika|Superpathway of L-methionine biosynthesis (transsulfuration).metabolika|Superpathway of L-methionine salvage and degradation.metabolika|Superpathway of L-phenylalanine and L-tyrosine biosynthesis.metabolika|Superpathway of L-phenylalanine biosynthesis.metabolika|Superpathway of L- serine and glycine biosynthesis I.metabolika|Superpathway of L-threonine biosynthesis.metabolika|Superpathway of L-threonine metabolism.metabolika|Superpathway of L- tryptophan biosynthesis.metabolika|Superpathway of L-tyrosine biosynthesis.metabolika|Superpathway of linalool biosynthesis.metabolika|Superpathway of linamarin and lotaustralin biosynthesis.metabolika|Superpathway of lipopolysaccharide biosynthesis.metabolika|Superpathway of lipoxygenase.metabolika|Superpathway of megalomicin A biosynthesis.metabolika|Superpathway of melatonin degradation.metabolika|Superpathway of menaquinol-10 biosynthesis.metabolika|Superpathway of menaquinol-11 biosynthesis.metabolika|Superpathway of menaquinol-12 biosynthesis.metabolika|Superpathway of menaquinol-13 biosynthesis.metabolika|Superpathway of menaquinol-6 biosynthesis I.metabolika|Superpathway of menaquinol-7 biosynthesis.metabolika|Superpathway of menaquinol-8 biosynthesis I.metabolika|Superpathway of menaquinol-8 biosynthesis II.metabolika|Superpathway of menaquinol-9 biosynthesis.metabolika|Superpathway of methanogenesis.metabolika|Superpathway of methylglyoxal degradation.metabolika|Superpathway of microbial D-galacturonate and D-glucuronate degradation.metabolika|Superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis.metabolika|Superpathway of NAD biosynthesis in eukaryotes.metabolika|Superpathway of neomycin biosynthesis.metabolika|Superpathway of nicotinate degradation.metabolika|Superpathway of nicotine biosynthesis.metabolika|Superpathway of oleoresin turpentine biosynthesis.metabolika|Superpathway of ornithine degradation.metabolika|Superpathway of penicillin, cephalosporin and cephamycin biosynthesis.metabolika|Superpathway of pentose and pentitol degradation.metabolika|Superpathway of phenylethylamine degradation.metabolika|Superpathway of phosphatidylcholine biosynthesis.metabolika|Superpathway of phospholipid biosynthesis I (bacteria).metabolika|Superpathway of phospholipid biosynthesis II (plants).metabolika|Superpathway of photosynthetic hydrogen production.metabolika|Superpathway of phylloquinol biosynthesis.metabolika|Superpathway of plastoquinol biosynthesis.metabolika|Superpathway of polyamine biosynthesis I.metabolika|Superpathway of polyamine biosynthesis II.metabolika|Superpathway of polyamine biosynthesis III.metabolika|Superpathway of pterocarpan biosynthesis (via daidzein).metabolika|Superpathway of pterocarpan biosynthesis (via formononetin).metabolika|Superpathway of purine deoxyribonucleosides degradation.metabolika|Superpathway of purine nucleotide salvage.metabolika|Superpathway of purine nucleotides de novo biosynthesis I.metabolika|Superpathway of purine nucleotides de novo biosynthesis II.metabolika|Superpathway of purines degradation in plants.metabolika|Superpathway of pyridoxal 5'- phosphate biosynthesis and salvage.metabolika|Superpathway of pyrimidine deoxyribonucleoside salvage.metabolika|Superpathway of pyrimidine deoxyribonucleosides degradation.metabolika|Superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli).metabolika|Superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis.metabolika|Superpathway of pyrimidine nucleobases salvage.metabolika|Superpathway of pyrimidine ribonucleosides degradation.metabolika|Superpathway of pyrimidine ribonucleosides salvage.metabolika|Superpathway of pyrimidine ribonucleotides de novo biosynthesis.metabolika|Superpathway of quinolone and alkylquinolone biosynthesis.metabolika|Superpathway of rifamycin B biosynthesis.metabolika|Superpathway of roquefortine, meleagrin and neoxaline biosynthesis.metabolika|Superpathway of rosmarinic acid biosynthesis.metabolika|Superpathway of salicylate degradation.metabolika|Superpathway of scopolin and esculin biosynthesis.metabolika|Superpathway of seleno-compound metabolism.metabolika|Superpathway of ss-D-glucuronide and D-glucuronate degradation.metabolika|Superpathway of stearidonate biosynthesis (cyanobacteria).metabolika|Superpathway of steroid hormone biosynthesis.metabolika|Superpathway of Supporting Information for Publication 56 sulfate assimilation and cysteine biosynthesis.metabolika|Superpathway of sulfide oxidation (Acidithiobacillus ferrooxidans).metabolika|Superpathway of sulfide oxidation (phototrophic sulfur bacteria).metabolika|Superpathway of sulfide oxidation (Starkeya novella).metabolika|Superpathway of sulfolactate degradation.metabolika|Superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae).metabolika|Superpathway of sulfur metabolism (Desulfocapsa sulfoexigens).metabolika|Superpathway of sulfur oxidation (Acidianus ambivalens).metabolika|Superpathway of taurine degradation.metabolika|Superpathway of testosterone and androsterone degradation.metabolika|Superpathway of tetracycline and oxytetracycline biosynthesis.metabolika|Superpathway of tetrahydrofolate biosynthesis and salvage.metabolika|Superpathway of tetrahydrofolate biosynthesis.metabolika|Superpathway of tetrahydroxyxanthone biosynthesis.metabolika|Superpathway of tetrathionate reduction (Salmonella typhimurium).metabolika|Superpathway of the 3-hydroxypropanoate cycle.metabolika|Superpathway of thiamine diphosphate biosynthesis I.metabolika|Superpathway of thiamine diphosphate biosynthesis II.metabolika|Superpathway of thiamine diphosphate biosynthesis III (eukaryotes).metabolika|Superpathway of thiosulfate metabolism (Desulfovibrio sulfodismutans).metabolika|Superpathway of trichothecene biosynthesis.metabolika|Superpathway of trimethylamine degradation.metabolika|Superpathway of ubiquinol-6 biosynthesis (eukaryotic).metabolika|Superpathway of ubiquinol-8 biosynthesis (prokaryotic).metabolika|Superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis.metabolika|Superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis.metabolika|Superpathway of unsaturated fatty acids biosynthesis (E. coli).metabolika|Superpathway of vanillin and vanillate degradation.metabolika|Superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation.metabolika|Superpathway of Clostridium acetobutylicum acidogenic fermentation.metabolika|Superpathway of Clostridium acetobutylicum solventogenic fermentation.metabolika|Superpathway of N-acetylglucosamine, N- acetylmannosamine and N-acetylneuraminate degradation.metabolika|Superpathway of N- acetylneuraminate degradation.metabolika|Superpathway of S-adenosyl-L-methionine biosynthesis.metabolika|Superpathway polymethylated quercetinquercetagetin glucoside biosynthesis (Chrysosplenium).metabolika|Superpathways of coenzyme A biosynthesis I.metabolika|Superpathways of coenzyme A biosynthesis III (mammals).metabolika|Syringate degradation.metabolika|Taxadiene biosynthesis (engineered).metabolika|Thiamine salvage II.metabolika|Toluene degradation I (aerobic) (via o-cresol).metabolika|Toluene degradation II (aerobic) (via 4-methylcatechol).metabolika|Toluene degradation III (aerobic) (via p-cresol).metabolika|Toluene degradation IV (aerobic) (via catechol).metabolika|Toluene degradation V (aerobic) (via toluene-cis-diol).metabolika|Toluene degradation VI (anaerobic).metabolika|Trans-lycopene biosynthesis I (bacteria).metabolika|UDP-D- xylose biosynthesis.metabolika|UDP-galactofuranose biosynthesis.metabolika|UDP-sugars interconversion.metabolika|Ureide biosynthesis.metabolika|Vibriobactin biosynthesis.metabolika|Wybutosine biosynthesis.metabolika - Search Mode: By Formula or Mass 2. By Mass Search Settings: - Mass Tolerance: 5 ppm 3. By Formula Search Settings: - Max. # of Predicted Compositions to be searched per Compound: 3 Supporting Information for Publication 57 4. Display Settings: - Max. # Pathways in 'Pathways' column: 20 ------------------------------------------------------------------ Processing node 36: Search Mass Lists ------------------------------------------------------------------ 1. Search Settings: - Mass Lists: Arita Lab 6549 Flavonoid Structure Database.masslist|Natural Products Atlas 2020_06.massList|2020-10 COMPLETE HML Library_V12.massList|Prodelphinidin Compound Database_RT_2018Apr25.massList|Polyphenol Compound Database_RT_01FA_2020Jul_PulseSeedCoats.massList - Mass Tolerance: 5 ppm - Use Retention Time: True - RT Tolerance [min]: 0.2 ------------------------------------------------------------------ Processing node 29: Predict Compositions ------------------------------------------------------------------ 1. Prediction Settings: - Mass Tolerance: 5 ppm - Min. Element Counts: C H - Max. Element Counts: C120 H240 N4 O150 P S - Min. RDBE: 0 - Max. RDBE: 40 - Min. H/C: 0.1 - Max. H/C: 4 - Max. # Candidates: 50 - Max. # Internal Candidates: 200 2. Pattern Matching: - Intensity Tolerance [%]: 30 - Intensity Threshold [%]: 0.1 - S/N Threshold: 3 - Min. Spectral Fit [%]: 30 Supporting Information for Publication 58 - Min. Pattern Cov. [%]: 90 - Use Dynamic Recalibration: True 3. Fragments Matching: - Use Fragments Matching: False - Mass Tolerance: 5 ppm - S/N Threshold: 3 ------------------------------------------------------------------ Processing node 25: Assign Compound Annotations ------------------------------------------------------------------ 1. General Settings: - Mass Tolerance: 5 ppm 2. Data Sources: - Data Source #1: MassList Search - Data Source #2: mzVault Search - Data Source #3: mzCloud Search - Data Source #4: Metabolika Search - Data Source #5: Predicted Compositions - Data Source #6: (not specified) - Data Source #7: (not specified) 3. Scoring Rules: - Use mzLogic: True - Use Spectral Distance: True - SFit Threshold: 20 - SFit Range: 20 ------------------------------------------------------------------ Processing node 22: Search mzCloud ------------------------------------------------------------------ 1. General Settings: Supporting Information for Publication 59 - Compound Classes: All - Precursor Mass Tolerance: 10 ppm - FT Fragment Mass Tolerance: 10 ppm - IT Fragment Mass Tolerance: 0.4 Da - Library: Autoprocessed; Reference - Post Processing: Recalibrated - Max. # Results: 10 - Annotate Matching Fragments: False 2. DDA Search: - Identity Search: HighChem HighRes - Match Activation Type: True - Match Activation Energy: Match with Tolerance - Activation Energy Tolerance: 40 - Apply Intensity Threshold: True - Similarity Search: Confidence Reverse - Match Factor Threshold: 50 3. DIA Search: - Use DIA Scans for Search: False - Max. Isolation Width [Da]: 500 - Match Activation Type: False - Match Activation Energy: Any - Activation Energy Tolerance: 100 - Apply Intensity Threshold: False - Match Factor Threshold: 20 ------------------------------------------------------------------ Processing node 37: Search mzVault ------------------------------------------------------------------ 1. Search Settings: Supporting Information for Publication 60 - mzVault Library: Bamba lab 34 lipid mediators library stepped NCE 10 30 45.db|Bamba lab 598 polar metabolites stepped NCE 10 30 45.db|Polyphenol_CG_oligomers_2018May4.db|PP_2018May9.db|Negative ion mode_Jan2021.db - Max. # Results: 10 - Match Factor Threshold: 50 - Search Algorithm: HighChem HighRes - Match Analyzer Type: True - IT Fragment Mass Tolerance: 0.4 Da - FT Fragment Mass Tolerance: 10 ppm - Use Retention Time: False - Precursor Mass Tolerance: 10 ppm - Apply Intensity Threshold: True - Match Ionization Method: True - Ion Activation Energy Tolerance: 50 - Match Ion Activation Energy: Match with Tolerance - Match Ion Activation Type: True - Compound Classes: All - Remove Precursor Ion: True - RT Tolerance [min]: 0.2 ------------------------------------------------------------------ Processing node 17: Differential Analysis ------------------------------------------------------------------ 1. General Settings: - Log10 Transform Values: True ------------------------------------------------------------------ Processing node 38: Descriptive Statistics ------------------------------------------------------------------ No parameters Filter This file contains the following filters: Supporting Information for Publication 61 Row Filter for Compounds: ------------------------------------ AND | +--BackgroundStatus is false | +--NormArea in any category | +--RT [min] is between 2.00 and 20.00 Study === Study: PatternedLentilSeedCoats_CD3.2_NoMottle_NoSpotted_NoGMarbled, 8/11/2021 10:39:17 PM === Directory: C:\Users\Public\Documents\Thermo\Compound Discoverer 3.2\Elessawy\PatternedSeedcoats_Mar2022 ------------------------------------------------------------------ Factors: ------------------------------------------------------------------ Sample number Options: 1, 4, 16, 93, 43, 258, 163, 174, 182, 211, 226, 310, 315, 44, 126, 210, 300, 136 Cotyledon color Options: Yellow, Red Field Options: Sutherland, Rosthern, Pullman Genotype Options: CDC Asterix AGL, CDC Greenstar AGL, CDC Redwing AGL, ILL 5883 AGL, DPL 62 AGL, PI 178971 LSP AGL, PI 431739 LSP AGL, PI 289079 LSP AGL, PI 298122 LSP AGL, PI 299116 LSP AGL, PI 320954 LSP AGL, PI 374116 LSP AGL, PI 490289 LSP AGL, PI 533693 LSP AGL, Eston AGL, Indianhead AGL, PI 320953 LSP AGL, PI 472488 LSP AGL Seed coat color Options: Green, Dark green, Black Seed coat pattern Options: Absent, Dotted, Marbled, Black Supporting Information for Publication 62 Seed size Options: M, XL, L, S ------------------------------------------------------------------ Samples and Files: ------------------------------------------------------------------ [S1] 190118QE_001 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_001.raw [S2] 190118QE_002 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_002.raw [S4] 190118QE_004 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_004.raw [S5] 190118QE_005 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_005.raw [S6] 190118QE_006 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_006.raw [S7] 190118QE_007 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_007.raw [S8] 190118QE_008 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_008.raw [S9] 190118QE_009 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_009.raw [S10] 190118QE_010 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_010.raw [S11] 190118QE_011 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] Supporting Information for Publication 63 E:\QE Data\2019Jan18\190118QE_011.raw [S12] 190118QE_012 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_012.raw [S13] 190118QE_013 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_013.raw [S14] 190118QE_014 [Sample number=1, Cotyledon color=Yellow, Field=Pullman, Genotype=CDC Asterix AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=M] E:\QE Data\2019Jan18\190118QE_014.raw [S15] 190118QE_015 [Sample number=4, Cotyledon color=Yellow, Field=Pullman, Genotype=CDC Greenstar AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=XL] E:\QE Data\2019Jan18\190118QE_015.raw [S16] 190118QE_016 [Sample number=16, Cotyledon color=Red, Field=Pullman, Genotype=CDC Redwing AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=M] E:\QE Data\2019Jan18\190118QE_016.raw [S17] 190118QE_017 [Sample number=43, Cotyledon color=Red, Field=Pullman, Genotype=DPL 62 AGL, Seed coat color=Green, Seed coat pattern=Dotted, Seed size=L] E:\QE Data\2019Jan18\190118QE_017.raw [S19] 190118QE_019 [Sample number=44, Cotyledon color=Yellow, Field=Pullman, Genotype=Eston AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=M] E:\QE Data\2019Jan18\190118QE_019.raw [S21] 190118QE_021 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_021.raw [S22] 190118QE_022 [Sample number=93, Cotyledon color=Red, Field=Pullman, Genotype=ILL 5883 AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=L] E:\QE Data\2019Jan18\190118QE_022.raw [S23] 190118QE_023 [Sample number=126, Cotyledon color=Yellow, Field=Pullman, Genotype=Indianhead AGL, Seed coat color=Black, Seed coat pattern=Black, Seed size=S] E:\QE Data\2019Jan18\190118QE_023.raw [S24] 190118QE_024 [Sample number=136, Cotyledon color=Red, Field=Pullman, Genotype=PI 178971 LSP AGL, Seed coat color=Green, Seed coat pattern=Dotted, Seed size=S] E:\QE Data\2019Jan18\190118QE_024.raw [S26] 190118QE_026 [Sample number=163, Cotyledon color=Yellow, Field=Pullman, Genotype=PI 289079 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=L] Supporting Information for Publication 64 E:\QE Data\2019Jan18\190118QE_026.raw [S27] 190118QE_027 [Sample number=174, Cotyledon color=Yellow, Field=Pullman, Genotype=PI 298122 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=M] E:\QE Data\2019Jan18\190118QE_027.raw [S28] 190118QE_028 [Sample number=182, Cotyledon color=Yellow, Field=Pullman, Genotype=PI 299116 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=S] E:\QE Data\2019Jan18\190118QE_028.raw [S29] 190118QE_029 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_029.raw [S31] 190118QE_031 [Sample number=211, Cotyledon color=Yellow, Field=Pullman, Genotype=PI 320954 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=L] E:\QE Data\2019Jan18\190118QE_031.raw [S33] 190118QE_033 [Sample number=226, Cotyledon color=Yellow, Field=Pullman, Genotype=PI 374116 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=M] E:\QE Data\2019Jan18\190118QE_033.raw [S35] 190118QE_035 [Sample number=258, Cotyledon color=Yellow, Field=Pullman, Genotype=PI 431739 LSP AGL, Seed coat color=Green, Seed coat pattern=Dotted, Seed size=M] E:\QE Data\2019Jan18\190118QE_035.raw [S37] 190118QE_037 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_037.raw [S38] 190118QE_038 [Sample number=300, Cotyledon color=Red, Field=Pullman, Genotype=PI 472488 LSP AGL, Seed coat color=Black, Seed coat pattern=Black, Seed size=S] E:\QE Data\2019Jan18\190118QE_038.raw [S39] 190118QE_039 [Sample number=310, Cotyledon color=Yellow, Field=Pullman, Genotype=PI 490289 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=L] E:\QE Data\2019Jan18\190118QE_039.raw [S40] 190118QE_040 [Sample number=315, Cotyledon color=Yellow, Field=Pullman, Genotype=PI 533693 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=M] E:\QE Data\2019Jan18\190118QE_040.raw [S41] 190118QE_041 [Sample number=1, Cotyledon color=Yellow, Field=Rosthern, Genotype=CDC Asterix AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=M] E:\QE Data\2019Jan18\190118QE_041.raw [S42] 190118QE_042 [Sample number=4, Cotyledon color=Yellow, Field=Rosthern, Genotype=CDC Greenstar AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=XL] Supporting Information for Publication 65 E:\QE Data\2019Jan18\190118QE_042.raw [S43] 190118QE_043 [Sample number=16, Cotyledon color=Red, Field=Rosthern, Genotype=CDC Redwing AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=M] E:\QE Data\2019Jan18\190118QE_043.raw [S44] 190118QE_044 [Sample number=43, Cotyledon color=Red, Field=Rosthern, Genotype=DPL 62 AGL, Seed coat color=Green, Seed coat pattern=Dotted, Seed size=L] E:\QE Data\2019Jan18\190118QE_044.raw [S45] 190118QE_045 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_045.raw [S47] 190118QE_047 [Sample number=44, Cotyledon color=Yellow, Field=Rosthern, Genotype=Eston AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=M] E:\QE Data\2019Jan18\190118QE_047.raw [S49] 190118QE_049 [Sample number=93, Cotyledon color=Red, Field=Rosthern, Genotype=ILL 5883 AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=L] E:\QE Data\2019Jan18\190118QE_049.raw [S50] 190118QE_050 [Sample number=126, Cotyledon color=Yellow, Field=Rosthern, Genotype=Indianhead AGL, Seed coat color=Black, Seed coat pattern=Black, Seed size=S] E:\QE Data\2019Jan18\190118QE_050.raw [S51] 190118QE_051 [Sample number=136, Cotyledon color=Red, Field=Rosthern, Genotype=PI 178971 LSP AGL, Seed coat color=Green, Seed coat pattern=Dotted, Seed size=S] E:\QE Data\2019Jan18\190118QE_051.raw [S53] 190118QE_053 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_053.raw [S54] 190118QE_054 [Sample number=163, Cotyledon color=Yellow, Field=Rosthern, Genotype=PI 289079 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=L] E:\QE Data\2019Jan18\190118QE_054.raw [S55] 190118QE_055 [Sample number=174, Cotyledon color=Yellow, Field=Rosthern, Genotype=PI 298122 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=M] E:\QE Data\2019Jan18\190118QE_055.raw [S56] 190118QE_056 [Sample number=182, Cotyledon color=Yellow, Field=Rosthern, Genotype=PI 299116 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=S] E:\QE Data\2019Jan18\190118QE_056.raw [S57] 190118QE_057 [Sample number=210, Cotyledon color=Red, Field=Rosthern, Genotype=PI 320953 LSP AGL, Seed coat color=Black, Seed coat pattern=Black, Seed size=S] Supporting Information for Publication 66 E:\QE Data\2019Jan18\190118QE_057.raw [S58] 190118QE_058 [Sample number=211, Cotyledon color=Yellow, Field=Rosthern, Genotype=PI 320954 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=L] E:\QE Data\2019Jan18\190118QE_058.raw [S60] 190118QE_060 [Sample number=226, Cotyledon color=Yellow, Field=Rosthern, Genotype=PI 374116 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=M] E:\QE Data\2019Jan18\190118QE_060.raw [S61] 190118QE_061 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_061.raw [S63] 190118QE_063 [Sample number=258, Cotyledon color=Yellow, Field=Rosthern, Genotype=PI 431739 LSP AGL, Seed coat color=Green, Seed coat pattern=Dotted, Seed size=M] E:\QE Data\2019Jan18\190118QE_063.raw [S65] 190118QE_065 [Sample number=300, Cotyledon color=Red, Field=Rosthern, Genotype=PI 472488 LSP AGL, Seed coat color=Black, Seed coat pattern=Black, Seed size=S] E:\QE Data\2019Jan18\190118QE_065.raw [S66] 190118QE_066 [Sample number=310, Cotyledon color=Yellow, Field=Rosthern, Genotype=PI 490289 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=L] E:\QE Data\2019Jan18\190118QE_066.raw [S67] 190118QE_067 [Sample number=315, Cotyledon color=Yellow, Field=Rosthern, Genotype=PI 533693 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=M] E:\QE Data\2019Jan18\190118QE_067.raw [S68] 190118QE_068 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_068.raw [S69] 190118QE_069 [Sample number=1, Cotyledon color=Yellow, Field=Sutherland, Genotype=CDC Asterix AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=M] E:\QE Data\2019Jan18\190118QE_069.raw [S70] 190118QE_070 [Sample number=4, Cotyledon color=Yellow, Field=Sutherland, Genotype=CDC Greenstar AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=XL] E:\QE Data\2019Jan18\190118QE_070.raw [S71] 190118QE_071 [Sample number=16, Cotyledon color=Red, Field=Sutherland, Genotype=CDC Redwing AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=M] E:\QE Data\2019Jan18\190118QE_071.raw [S72] 190118QE_072 [Sample number=43, Cotyledon color=Red, Field=Sutherland, Genotype=DPL 62 AGL, Seed coat color=Green, Seed coat pattern=Dotted, Seed size=L] Supporting Information for Publication 67 E:\QE Data\2019Jan18\190118QE_072.raw [S74] 190118QE_074 [Sample number=44, Cotyledon color=Yellow, Field=Sutherland, Genotype=Eston AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=M] E:\QE Data\2019Jan18\190118QE_074.raw [S76] 190118QE_076 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_076.raw [S77] 190118QE_077 [Sample number=93, Cotyledon color=Red, Field=Sutherland, Genotype=ILL 5883 AGL, Seed coat color=Green, Seed coat pattern=Absent, Seed size=L] E:\QE Data\2019Jan18\190118QE_077.raw [S78] 190118QE_078 [Sample number=126, Cotyledon color=Yellow, Field=Sutherland, Genotype=Indianhead AGL, Seed coat color=Black, Seed coat pattern=Black, Seed size=S] E:\QE Data\2019Jan18\190118QE_078.raw [S79] 190118QE_079 [Sample number=136, Cotyledon color=Red, Field=Sutherland, Genotype=PI 178971 LSP AGL, Seed coat color=Green, Seed coat pattern=Dotted, Seed size=S] E:\QE Data\2019Jan18\190118QE_079.raw [S81] 190118QE_081 [Sample number=163, Cotyledon color=Yellow, Field=Sutherland, Genotype=PI 289079 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=L] E:\QE Data\2019Jan18\190118QE_081.raw [S82] 190118QE_082 [Sample number=174, Cotyledon color=Yellow, Field=Sutherland, Genotype=PI 298122 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=M] E:\QE Data\2019Jan18\190118QE_082.raw [S83] 190118QE_083 [Sample number=182, Cotyledon color=Yellow, Field=Sutherland, Genotype=PI 299116 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=S] E:\QE Data\2019Jan18\190118QE_083.raw [S84] 190118QE_084 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_084.raw [S85] 190118QE_085 [Sample number=210, Cotyledon color=Red, Field=Sutherland, Genotype=PI 320953 LSP AGL, Seed coat color=Black, Seed coat pattern=Black, Seed size=S] E:\QE Data\2019Jan18\190118QE_085.raw [S86] 190118QE_086 [Sample number=211, Cotyledon color=Yellow, Field=Sutherland, Genotype=PI 320954 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=L] E:\QE Data\2019Jan18\190118QE_086.raw [S91] 190118QE_090 [Sample number=226, Cotyledon color=Yellow, Field=Sutherland, Genotype=PI 374116 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=M] Supporting Information for Publication 68 E:\QE Data\2019Jan18\190118QE_090.raw [S93] 190118QE_092 [Sample number=258, Cotyledon color=Yellow, Field=Sutherland, Genotype=PI 431739 LSP AGL, Seed coat color=Green, Seed coat pattern=Dotted, Seed size=M] E:\QE Data\2019Jan18\190118QE_092.raw [S95] 190118QE_094 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_094.raw [S96] 190118QE_095 [Sample number=300, Cotyledon color=Red, Field=Sutherland, Genotype=PI 472488 LSP AGL, Seed coat color=Black, Seed coat pattern=Black, Seed size=S] E:\QE Data\2019Jan18\190118QE_095.raw [S97] 190118QE_096 [Sample number=310, Cotyledon color=Yellow, Field=Sutherland, Genotype=PI 490289 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=L] E:\QE Data\2019Jan18\190118QE_096.raw [S98] 190118QE_097 [Sample number=315, Cotyledon color=Yellow, Field=Sutherland, Genotype=PI 533693 LSP AGL, Seed coat color=Dark green, Seed coat pattern=Marbled, Seed size=M] E:\QE Data\2019Jan18\190118QE_097.raw [S99] 190118QE_098 [Sample number=210, Cotyledon color=Red, Field=Pullman, Genotype=PI 320953 LSP AGL, Seed coat color=Black, Seed coat pattern=Black, Seed size=S] E:\QE Data\2019Jan18\190118QE_098.raw [S101] 190118QE_100 [Sample number=n/a, Cotyledon color=n/a, Field=n/a, Genotype=n/a, Seed coat color=n/a, Seed coat pattern=n/a, Seed size=n/a] E:\QE Data\2019Jan18\190118QE_100.raw Grouping and Ratios ------------------------------------------------------------------ Grouping: ------------------------------------------------------------------ Study variable(s) for grouping: Seed coat color;Seed coat pattern ------------------------------------------------------------------ Sample Groups: ------------------------------------------------------------------ Black, Black Supporting Information for Publication 69 F23: Sample, 126, Yellow, Pullman, Indianhead AGL, Black, Black, S F38: Sample, 300, Red, Pullman, PI 472488 LSP AGL, Black, Black, S F50: Sample, 126, Yellow, Rosthern, Indianhead AGL, Black, Black, S F57: Sample, 210, Red, Rosthern, PI 320953 LSP AGL, Black, Black, S F65: Sample, 300, Red, Rosthern, PI 472488 LSP AGL, Black, Black, S F78: Sample, 126, Yellow, Sutherland, Indianhead AGL, Black, Black, S F85: Sample, 210, Red, Sutherland, PI 320953 LSP AGL, Black, Black, S F96: Sample, 300, Red, Sutherland, PI 472488 LSP AGL, Black, Black, S F99: Sample, 210, Red, Pullman, PI 320953 LSP AGL, Black, Black, S Dark green, Marbled F26: Sample, 163, Yellow, Pullman, PI 289079 LSP AGL, Dark green, Marbled, L F27: Sample, 174, Yellow, Pullman, PI 298122 LSP AGL, Dark green, Marbled, M F28: Sample, 182, Yellow, Pullman, PI 299116 LSP AGL, Dark green, Marbled, S F31: Sample, 211, Yellow, Pullman, PI 320954 LSP AGL, Dark green, Marbled, L F33: Sample, 226, Yellow, Pullman, PI 374116 LSP AGL, Dark green, Marbled, M F39: Sample, 310, Yellow, Pullman, PI 490289 LSP AGL, Dark green, Marbled, L F40: Sample, 315, Yellow, Pullman, PI 533693 LSP AGL, Dark green, Marbled, M F54: Sample, 163, Yellow, Rosthern, PI 289079 LSP AGL, Dark green, Marbled, L F55: Sample, 174, Yellow, Rosthern, PI 298122 LSP AGL, Dark green, Marbled, M F56: Sample, 182, Yellow, Rosthern, PI 299116 LSP AGL, Dark green, Marbled, S F58: Sample, 211, Yellow, Rosthern, PI 320954 LSP AGL, Dark green, Marbled, L F60: Sample, 226, Yellow, Rosthern, PI 374116 LSP AGL, Dark green, Marbled, M F66: Sample, 310, Yellow, Rosthern, PI 490289 LSP AGL, Dark green, Marbled, L F67: Sample, 315, Yellow, Rosthern, PI 533693 LSP AGL, Dark green, Marbled, M F81: Sample, 163, Yellow, Sutherland, PI 289079 LSP AGL, Dark green, Marbled, L F82: Sample, 174, Yellow, Sutherland, PI 298122 LSP AGL, Dark green, Marbled, M F83: Sample, 182, Yellow, Sutherland, PI 299116 LSP AGL, Dark green, Marbled, S F86: Sample, 211, Yellow, Sutherland, PI 320954 LSP AGL, Dark green, Marbled, L F91: Sample, 226, Yellow, Sutherland, PI 374116 LSP AGL, Dark green, Marbled, M F97: Sample, 310, Yellow, Sutherland, PI 490289 LSP AGL, Dark green, Marbled, L Supporting Information for Publication 70 F98: Sample, 315, Yellow, Sutherland, PI 533693 LSP AGL, Dark green, Marbled, M Green, Absent F14: Sample, 1, Yellow, Pullman, CDC Asterix AGL, Green, Absent, M F15: Sample, 4, Yellow, Pullman, CDC Greenstar AGL, Green, Absent, XL F16: Sample, 16, Red, Pullman, CDC Redwing AGL, Green, Absent, M F19: Sample, 44, Yellow, Pullman, Eston AGL, Green, Absent, M F22: Sample, 93, Red, Pullman, ILL 5883 AGL, Green, Absent, L F41: Sample, 1, Yellow, Rosthern, CDC Asterix AGL, Green, Absent, M F42: Sample, 4, Yellow, Rosthern, CDC Greenstar AGL, Green, Absent, XL F43: Sample, 16, Red, Rosthern, CDC Redwing AGL, Green, Absent, M F47: Sample, 44, Yellow, Rosthern, Eston AGL, Green, Absent, M F49: Sample, 93, Red, Rosthern, ILL 5883 AGL, Green, Absent, L F69: Sample, 1, Yellow, Sutherland, CDC Asterix AGL, Green, Absent, M F70: Sample, 4, Yellow, Sutherland, CDC Greenstar AGL, Green, Absent, XL F71: Sample, 16, Red, Sutherland, CDC Redwing AGL, Green, Absent, M F74: Sample, 44, Yellow, Sutherland, Eston AGL, Green, Absent, M F77: Sample, 93, Red, Sutherland, ILL 5883 AGL, Green, Absent, L Green, Dotted F17: Sample, 43, Red, Pullman, DPL 62 AGL, Green, Dotted, L F24: Sample, 136, Red, Pullman, PI 178971 LSP AGL, Green, Dotted, S F35: Sample, 258, Yellow, Pullman, PI 431739 LSP AGL, Green, Dotted, M F44: Sample, 43, Red, Rosthern, DPL 62 AGL, Green, Dotted, L F51: Sample, 136, Red, Rosthern, PI 178971 LSP AGL, Green, Dotted, S F63: Sample, 258, Yellow, Rosthern, PI 431739 LSP AGL, Green, Dotted, M F72: Sample, 43, Red, Sutherland, DPL 62 AGL, Green, Dotted, L F79: Sample, 136, Red, Sutherland, PI 178971 LSP AGL, Green, Dotted, S F93: Sample, 258, Yellow, Sutherland, PI 431739 LSP AGL, Green, Dotted, M n/a, n/a Supporting Information for Publication 71 F1: Blank, n/a, n/a, n/a, n/a, n/a, n/a, n/a F2: Blank, n/a, n/a, n/a, n/a, n/a, n/a, n/a F4: Blank, n/a, n/a, n/a, n/a, n/a, n/a, n/a F5: Blank, n/a, n/a, n/a, n/a, n/a, 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n/a, n/a, n/a, n/a, n/a F101: QualityControl, n/a, n/a, n/a, n/a, n/a, n/a, n/a ------------------------------------------------------------------ Ratios: ------------------------------------------------------------------ (Black, Black) / (Dark green, Marbled) (Black, Black) / (Green, Absent) (Black, Black) / (Green, Dotted) (Dark green, Marbled) / (Green, Absent) (Dark green, Marbled) / (Green, Dotted) Supporting Information for Publication 72 (Green, Dotted) / (Green, Absent)