High Resolution LC-MS Data Output and Analysis

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1 High Resolution LC-MS Data Output and Analysis

2 Your Sample LC/MS Result Sample Sample Efficient Separation Preparation Introduction Gradient (column) Today Data (computer) LC- MS Ions Detection Ions Separation Ionization MS Interface UV Spectra

3 Mass Spectrometer 1. Breaks up constituents into molecular ions and other fragments 2. The ions are separated according to their mass-to-charge ratio (m/z) 3. Measures masses

4 Mass Spectrometer 4. Structural information on metabolite * fragmentation pattern * accurate mass

5 Alternative Ionization Modes Atmospheric Pressure Ionization (API), in LC-MS Electrospray Ionisation (ESI): polar and semi-polar Atmospheric Pressure Chemical Ionization (APCI): less polar APCI ES lipids polarity of analyte molecule water

6 Positive or Negative Modes? The formation of positive or negative ions depends on the sign of the applied electrical field ES+: (M+H) + Good ionization of basic compounds (get proton) E.g. amino, amide, ester, aldehyde/keto functional groups (formic acid in sample solution to help ionize) ES-: (M-H) - Acidic Compounds (give proton) E.g. organic acids, containing OH (ammonium buffer in sample solution to help ionize)

7 Mass Analyzers Ion Cyclotron (FT-ICR-MS) Time of Flight (TOF) High Resolution Instruments Magnetic Sector Quadrupole Ion Trap Quadrupole Low Resolution Instruments

8 Mass Analyzers Ion Cyclotron (FT-ICR-MS) Mass Accuracy <1ppm Time of Flight (TOF) 3-1ppm Magnetic Sector 2-5ppm Quadrupole Ion Trap Quadrupole n/a n/a

9 LC-PDA-QTOF-MS of a Tomato Sample PDA-sample MS-reference (lock mass) injected every few scans (TIC) MS-sample - Total Ion Chromatogram (TIC)

10 Spectra Obtained at Each Scan PDA-sample MS-reference (lock mass) Enkephalin ( in ES+) MS-sample

11 Extracted chromatogram of a Specific Ion Extracted chromatogram at m/z 33 Extracted chromatogram at m/z 611 TIC

12 LC/UV/MS Chromatograms of Standard s Mixture (UV at 24nm, ES+ and ES-) Standard Mix MixAllStand_b1 8.e-1 6.e-1 AU 4.e-1 2.e Jan-26 3: Diode Array Range: MixAllStand_b1 1 TIC e ILMixAllStand-c UV MS (+) Time 1-Jan-26 1: TOF MS ES- TIC 8.88e3 MS (-) Chlorogenic acid 2 Caffeic acid 3 Rutin 4 p-coumaric 5 Quercetin-3-glucoside 6 Ferulic acid 7 Sinapic acid 8 Benzoic acid 9 Morin (Internal Standard) 1 Tomatin 11 Quercetin 12 Cinnamic acid 13 Naringenin Chalcone 14 Naringenin 15 Kaempferol Time

13 In the Spectra: Molecular Ion -An unfragmented (parent) ion formed by loss or gain of an proton from a molecule - Has the same mass as the metabolite being analyzed (+ H or - H) The Molecular Ion

14 Chromatogram and Spectrum of Morin ES(-) [M-H] - ES(+) [M+H] + Chromatograms in ES(+) & ES(-) modes Spectra's in ES(+) & ES(-) modes

15 Adduct Formation in Spectra (Na) Rutin C 27 H 3 O 16 [M+Na] + C 27 H 3 O 16 Na C 27 H 31 O 16 [M+H] + Na (22)

16 S5 Typical Adducts formed in LCMS Adducts Ion [ M+CH 3 COO ] - Source of Adduct Acetic acid Mass of Adduct Ion M+59 [ M+Cl ] - Chlorinated solvent M+35 [ M+NH 4 ] + [ M+Na ] + [ M+K ] + Ammonia Sodium Salt Potassium Salt M+18 M+23 M+39 [ M+CH 3 CNH ] + [ M+CH Methanol M+33 3 OHH ] + Acetonitrile M+42 [ M+H 2 O] + Water M+19

17 Isotopes in Spectra ( 13 C) Rutin C 27 H 3 O 16 [M+Na] + C 27 H 3 O 16 Na 13 C (little from other isotopes H, O) C 27 H 31 O 16 [M+H] +

18 Abundance of Isotopes (in Spectra)

19 An example of how isotopes can aid in peak identification A (5.6) A + 2 (49.3) The ratio of peaks containing 79 Br and its isotope 81 Br (/98) confirms the presence of bromine in the compound.

20 Fragments of a Metabolite in Spectra MS spectrum of Rutin in ES(+) Quercetin [M+Na] + Glucose [M+H] + Rhamnose Glucose (162) Rhamnose (146)

21 Spectra Components Molecular Ion Fragments of Metabolite Adducts (from solvent or di-tri tri-mers) Isotopes

22 Spectrum of Quercetin Trisaccharide (a Rutin Derivative) loss of pentose residue = [M+Na] + Rutin Quercetin [M+H] sugar UV spectra of Rutin and Quercetin Trisaccharide Rutin m/z

23 Mass Accuracy and Structure Elucidation High mass accuracy (1 mda) Low mass accuracy ( mda)

24 Mass Accuracy and Structure Elucidation Selected natural compounds with formula C 18 H 19 NO (monoisotopic mass Da)

25 Performing MS-MS: MS-MS of m/z 435 at different collision energies CE=3 ev CE=15 ev CE=1 ev CE=5 ev

26 Output Data For High Res. LC-MS Based Metabolomics Nominal Accurate

27 Software for comparing full-scan datasets MetAlign method Peak picking Alignment Statistics

28 Software for comparing full-scan datasets MarkerLynx method

29 Out-put from the MarkerLynx (Waters) Program : Analyses of Wild-Type Tomato Peel (Different Stages of Development; ES+) Samples Processed Markers Detected TIC of currently selected sample Response of a marker across all samples Principle Components Analysis Markers responsible for clustering (by PCA)

30 A Case Study in Tomato Small Green Middle Green Big Green Breaker Orange Red

31 Sample Preparation for Tomato Fruit Metabolome Analysis Harvesting tomato fruit at different developmental stages Separation of peel and flesh tissues Immediate freezing in liquid nitrogen Grinding to fine powder Weighing frozen samples Extraction in MeOH by vortexing and sonication Analyzing with UPLC-MS [ ES (+) and ES (-) ]

32 Experimental Set-Up for LC-MS Analysis: PEEL and FLESH during tomato fruit development Green stage Flesh Peel ES+ ES- ES+ ES- ES+ ES- ES+ ES- Breaker stage Flesh Peel Orange stage Flesh Peel Red stage Flesh Peel ES+ ES- ES+ ES- ES+ ES- ES+ ES-

33 UPLC-Q-Tof-MS Analysis of Four Stages of Tomato Fruit Development Tom_24_WTa AU 5.e-1 Tom_22_WTa AU AU 5.e-1 Tom_18_WTa AU e Jan-26 3: Diode Array Range: : Diode Array Range: e Tom_2_WTa5 3: Diode Array Range: Red Orange Breaker 3: Diode Array Range: 3.2 Green Time Tom_24_WTa Jan-26 TIC 5.e Tom_22_WTa6 TIC 5.e Tom_2_WTa5 TIC 5.e Tom_18_WTa TIC 5.e Red Orange Breaker Green Time UV (24 nm) MS (ES(+),TIC)

34 Out-put from the MarkerLynx (Waters) Program : Analyses of Wild-Type Tomato Peel (Different Stages of Development; ES+)

35 Peel-Flesh Profiles During Fruit Development Red flesh Red peel Orange peel Component 2 Orange flesh Breaker flesh Breaker peel Green flesh Green peel Comp. 1

36 Wild-type Tomato Peel, Different Developmental Stages Red DOWN NO CHANGE9-Jan-26 Tom_24_WTa7 UP 9-Jan-26 Tom_24_WTa7 Tom_24_WTa e4 Area 731 Area Tom_22_WTa e4 Area Tom_22_WTa Area Tom_22_WTa Jan e4 Area e4 Area Orange Breaker Tom_2_WTa Tom_18_WTa e4 Area e4 Area Tom_2_WTa Area Tom_18_WTa Area Tom_2_WTa e4 Area Tom_18_WTa e4 Area Green Time Time Time Tomatine Rutin & Quercetin trisacharide Naringenin chalcone

37 Tomato (var. Ailsa Craig) and the Mutant Y, at different ripening stages Green Breaker Orange Red Wild-Type Mutant Y Tomato peel of Mutant Y and Wild-type

38 Biosynthesis of Naringenin Chalcone in the Flavonoid Pathway Phenylalanine Cinnamate Coumarate Coumaroyl - CoA Chalcone synthase (CHS) Naringenin chalcone Naringenin Lignins, Coumarins, Chlorogenic-acid Anthocyanines Flavonols Condensed tannins

39 Experimental Set-Up for LC-MS Analysis: PEEL and FLESH during Y fruit development Y Green stage Flesh Peel ES+ ES- ES+ ES- ES+ ES- ES+ ES- Y Breaker stage Flesh Peel Y Orange stage Flesh Peel Y Red stage Flesh Peel ES+ ES- ES+ ES- ES+ ES- ES+ ES-

40 HPLC-QTOF QTOF-MS (Ultima-PRI) - Wild Type and Y Peels 1 st principal component (X axis) - developmental stage (47.1) 2 nd principal component (Y axis) mutation (9.4) WT-Orange All breaker WT- Red Y -Orange All green Y -Red

41 UV and MS Chromatograms of Red Tomato Peel (Wild Type and Mutant Y ) Tom_56_WTa Mutant Y Jan-26 TIC 2.11e4 Tom_56_WTa AU Mutant Y 3.25 IS 9-Jan-26 3: Diode Array Range: Tom_8_WTa3.85 TIC 2.12e4.7 Wild Type e Tom_8_WTa3 3: Diode Array.8 Range: Wild Type Time AU e Time UV (24 nm) MS (ES(+),TIC)

42 The Yellow Pigment Absent in the Y Mutant Fruit Peel is Naringenin Chalcone Tom_8_WTa TIC 1.37e e Tomato peel Tomato peel MixAllStand_b TIC e e3 Standard s mixture Naringenin Chalcone Standard Time m/z Cinnamic acid 13 Naringenin Chalcone 14 Naringenin 15 Kaempferol

43 Unknown Mass peak (RT=3.51 min) Detected Only in Wild Type Tom_72_WTa Jan Tom_56_WTa Tom_4_WTa Tom_24_WTa7 Tom_8_WTa Time Mutant Y Mutant Y Wild Type Wild Type Wild Type Extracted mass chromatogram at m/z Da

44 Unknown Mass peak Detected in Higher Levels in Y Mut. Y Mut. Y Wild-type Wild type Wild type Tom_72_WTa Tom_56_WTa Jan e3 Area Tom_4_WTa e3 Area Tom_24_WTa e3 Area Tom_8_WTa e3 Area e3 Area Time Extracted mass chromatogram at m/z Da

45 In-depth Analysis of Red Tomato Peel (ES+) Wild-type vs. the Y Mutant MarkerLynx Differential Markers - Filtering out non-replicated data - Identifying molecular ions, isotopes, adducts, fragments and passing from Markers to Metabolites - Analysis of differential metabolites and identification

46 What are the Differentially Expressed Metabolites between WT and Y? Peak assignment by: - Accurate mass and elemental composition (MassLynx and natural products database) - MS-MS fragmentation - UV spectrum - Literature - UV & MS spectra databases (e.g. for tomato in PRI)

47 Differential Metabolites between the "Y" and Wild Type Peel UPLC-QTOF-MS in ES- Mode Differential metabolites (ES-) R only O only Both R & O Total WT > "Y" "Y" > WT

48 Differential Metabolites between the "Y" and Wild Type Peel UPLC-QTOF-MS in ES+ Mode Differential metabolites (ES+) R only O only Both R & O Total WT >"Y" "Y" > WT

49 What are the Differentially Expressed Metabolites between WT and Y? Most mass peaks showing higher levels in WT than in the Y mutant are derivatives of Naringenin Chalcone or Naringenin.

50 Biosynthesis of Naringenin Chalcone in the Flavonoid Pathway Phenylalanine Isomers (identical mass) Cinnamate Coumarate Coumaroyl - CoA Chalcone synthase (CHS) Naringenin chalcone Naringenin Lignins, Coumarins, Chlorogenic-acid Anthocyanines Flavonols Condensed tannins

51 Hydroxylated Naringenin & Naringenin- Chalcone Ilana wt-tom rp 23 M5983 Y HPLC-QTOF Da 875 M WT Da Time

52 UV Spectra of Differential Peaks (35.7 min. and 37.5 min.) AU 1.e-2 8.e-3 6.e-3 4.e Naringenin 1.126e-2 AU 6.e-1 4.e-1 2.e e-1 Naringenin Chalcone 2.e-3.. M (35.667) Cm (2131: :216) e-3 1.5e-3 1.e-3 5.e-4 AU 3: Diode Array 2.195e-3 Peak at 35.7 min M (36.9) Cm (229-( )) AU 4.e-3 2.e-3 3: Diode Array 5.444e-3 Peak at 37.5 min nm. nm

53 Spectra of differential compounds at RT=35.79 min and 37.5 min RT=35.79 min RT=37.5 min

54 Elemental Composition ( ) Elemental composition: C 15 H 12 O 6 for neutral compound Elemental composition of Naringenin: C 15 H 12 O 5 Difference: OH group instead of H

55 Suggested Metabolite MS-MS Fragmentation of m/z Eriodictyol (C 15 H 12 O 6 ) Main fragmentations in reference: I. J. M. S. 247 (25) MS-MS fragmentation of m/z m/z

56 Naringenin and Naringenin Chalcone Glycosides HPLC-QTOF Ilana Y-tom rp 55 M Da 1.41e M Y WT Da 1.41e Time

57 UV Spectra of Peak at 32.8 min. and Naringenin Chalcone M (42.483) Cm (2544-( )) AU 6.e e-1 3: Diode Array 6.774e-1 Peak at 32.8 min 2.e-1. M (32.65) Cm (1954-( )) : Diode Array 3.933e-3 AU 3.e-3 2.e-3 Naringenin Chalcone 1.e nm

58 MS spectra at RT=28, 3 32 and 33 min RT=28.7 min For MS-MS RT=3.5 min Exact mass of shows elemental composition of C 21 H 22 O 1 RT=32.8 min RT=33.4 min

59 MS-MS Fragmentation of m/z for Peak at RT=32.8 Peak at 32.8 M67 47 (33.469) Cm (45:411) Naringenin Chalcone Naringenin Chalcone-hexose 2: TOF MSMS ES+ 1.59e Hexose (m/z 162) m/z

60 Mass Peak at RT=43.4min (>WT) MS spectra at RT=43.4min Selected Mass Chromatogram m/z 33.8 Da TIC chromatogram Mut Mut Mut WT WT WT

61 Methyl ether of Hydroxylated Naringenin and Naringenin Chalcone Peaks at 43.4 min and 44.6 min - Calculated formula is C 16 H 14 O 6 based on exact mass - Proposed structure for the peak at 43.4 min: Hesperetin or a B-ring positional isomer

62 MS-MS Fragmentation of m/z 33.8 (43.4 min.) Ilana wt-tom rp 23 msms M67 55 (43.325) Cm (55:56) : TOF MSMS 33.8ES [M+H] [M+H-H 2 O] m/z Hesperetin

63 Proposed Scheme of Naringenin & Naringenin Chalcone Hydroxylation, Methylation and Glycosylation Glycosylation OH HO OH OH O Naringenin Chalcone HO O B A C OH O Naringenin OH OH OH OH O OH O OH OH Glycosylation e.g. Naringenin glucoside O O OH OH OH OH Glycosylation HO OH HO O Glycosylation OH O Hydroxylated Naringenin Chalcone OH O Hydroxylated Naringenin e.g. Eriodyctyol or a B-ring isomer OH OMe OH OMe Glycosylation HO OH HO O Glycosylation OH O OH O Methyl ether of Hydroxylated Naringenin Chalcone Methyl ether of Hydroxylated Naringenin e.g.hesperetin or a B-ring isomer

64 Biosynthesis of Naringenin Chalcone in the Flavonoid Pathway Phenylalanine Cinnamate Coumarate Coumaroyl - CoA Chalcone synthase (CHS) Naringenin chalcone Naringenin Lignins, Coumarins, Chlorogenic-acid Anthocyanines Flavonols Condensed tannins

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