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14 protocols using it tof

1

UPLC-DAD-ESI-IT-TOF Metabolite Analysis

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The UPLC-DAD-ESI-IT-TOF analysis of the metabolites was performed using Shimadzu LC-30AD instrument equipped with two LC-30AD pumps, an SIL-30AC autosampler, SPD-M20A, CTO-20AC column oven, and CBM-20A system controller, and coupled to an IT-TOF mass spectrometer with an ESI interface.
The chromatography separations were performed on a Shim-pack HR-ODS column (150 mm × 2.1 mm, 3 μm). The column was eluted with a gradient mobile phase A of water-formic acid (100: 0.1, v/v) and B of acetonitrile, The elution gradient was 0–2 min, 5–10% B, 2–4 min, 10–12% B, 4–7 min, 12–18% B, 7–13 min, 18–27% B, 13–32 min, 27–56% B, 32–37 min, 56–100% B, and 37–47 min 100% B. The flow rate was 0.2 mL/min; the injection volume was 5 μL and the column oven temperature was kept at 30°C.
The tandem mass spectrometry analyses were carried out on an IT-TOF (Shimadzu, Japan) with the full scan over m/z 100–900 (MS1) and m/z 50–900 (MS2 and MS3) in the ion model of negative(NI) and positive(PI). The parameters were as follows: heat block and curved desolvation line temperature, 200°C; nebulizing nitrogen gas flow, 1.5 L/min; interface voltage: (+), 4.5 kv; (−), 3.5 kv; detector voltage, 1.56 kv; relative collision-induced dissociation energy, 50%.
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2

Lipid Extraction and Quantification

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Plasma was sonicated and extracted with chloroform/methanol/Tris-HCl 50 mmol/L pH 7.5 (2 : 1 : 1, vol/vol) containing internal standards ([H2]8 AEA 5 pmol; [H2]5 2-AG, [H2]5 PEA, and [H2]4 OEA 50 pmol each) for EC quantification as well as 1,2-heptadecanoin (Larodan AB, Malmo, Sweden) for DAG measurement. The lipid-containing organic phase was dried down, weighed, and prepurified by open-bed chromatography on silica gel with 99 : 1, 90 : 10, and 50 : 50 (v/v) chloroform/methanol. The 90 : 10 fraction was used for EC and N-acylethanolamine quantification by LC-APCI-MS (LCMS-2020, Shimadzu) as previously reported [54 (link)]. DAG levels were measured by LC-MS-MS using an LC20AB coupled to a hybrid detector IT-TOF (Shimadzu Corporation, Kyoto, Japan) equipped with an ESI interface [55 (link)].
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3

Quantitative Analysis of Leaf Metabolites

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Ground leaf tissue was weighed and collected into 200 µl methanol containing 40 µM caffeine or 10 µM esculin as an internal standard and incubated at 60 °C for 2 hours. After a 30 minute centrifugation step at 5000 g, an aliquot of the supernatant (25 µl) was mixed with an equal volume of water and analyzed on a Thermo-Finnigan instrument equipped with a Deca XP ion trap detector or a Shimadzu IT-TOF. In both systems the column used was a Phenomenex Kinetic 5 µ C18 100A (100 x 2.10 mm x 5 µm) and the binary solvent system consisted of acetonitrile (ACN) and 0.1% formic acid in water. The elution program was as follows: 1 minute isocratic at 12% ACN, 3.5 minute gradient up to 25% ACN, 2.5 minute gradient up to 50% ACN, 1 minute gradient up to 100% ACN, 6 minute isocratic at 100% ACN, 1 minute gradient down to 12% ACN, and 2.5 minute isocratic at 12% ACN. Peak areas were calculated using the ICIS algorithm in Finnigan’s Xcalibur software or LCMS solutions and normalized by leaf mass (fresh weight) and the peak area of the internal standard.
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4

Synthesis and Characterization of Tryptanthrins and Quingdainones

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All the commercially available chemicals were used without further purification. NMR spectra were recorded on a JEOL ECS-400 (400 MHz, Japan). Chemical shifts are reported in ppm and refer to residual protons in the deuterated solvent as the internal standard. IR spectra were recorded on a Nicolet 380 FT-IR (Thermo Scientific, England). UV/VIS-spectra were recorded on a Specord 210 (Analytik Jena, Jena, Germany). Mass spectrometry was performed on an IT-TOF from Shimadzu, Japan with direct injection of the samples. For the original NMR, IR and mass spectrometry of compounds, please see the Supplementary Materials. Flash purification was performed with a Puriflash 4250-250 from Interchim, France.
Tryptanthrins 4, which are initially needed, were prepared with isatin 5 and isatoic anhydride according to Bergman et al. [37 (link)], which is extendable to all commercially available isatins. For tryptanthrin derivatives with substituents at positions 1–4 (R’ 2’-5’ in quingdainones), another method was used due to the unavailability of various isatoic acids. 2-Chloroisatins 6 were prepared according to Grimshaw et al. [38 (link)]. These 2-chloroisatins reacted with 2-aminobenzoic acids at 130 °C in DMF to form tryptanthrins without any further additives [39 (link)]. Unsubstituted quingdainone was obtained according to [12 (link)].
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5

Reversed-Phase HPLC-DAD Analysis

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Analyses were performed with an Interface-Time of Flight (IT-TOF), Shimadzu using electronspray (ESI) ionization. The peaks were separated in the C-18 reversed-phase HPLC column (Waters, USA). The solvent system consisted of 10% to 100% acetonitrile (v/v) for 15 min, gradiently at a flow rate of 0.5 mL/min. The detection was accomplished using a Diode Array Detection system (DAD) Series SPD-M20A (Shimadzu). The PDA data was shown the signal at a wavelength of 254 and 350 nm.
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6

NMR Characterization of Platinum Complexes

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1H NMR (400 MHz), 19F{1H} (376 MHz), 31P{1H} NMR (162 MHz) and 195Pt{1H} (86 MHz) spectra were recorded on a Bruker Avance instrument at 295 K. All chemical shifts (δ) are reported in ppm relative to their corresponding external standards (SiMe4 for 1H, CFCl3 for 19F{1H}, 85% H3PO4 for 31P{1H}, Na2PtCl6 for 195Pt{1H}) and the coupling constants (J) have being expressed in Hz. The instrument for HR ESI-Mass measurement was a Shimadzu IT-TOF with an electrospray ionization source, which is part of the Arkansas Statewide Mass Spectrometry Facility. The 2-(2,4-difluorophenyl)pyridine (dfppy), bis(diphenylphosphino)methane (dppm), 1,2-bis(diphenylphosphino)ethane (dppe) and 1,2-bis(diphenylphosphino)benzene (dppbz) and all the other chemicals were purchased from commercial resources. All the reactions were carried out under Argon atmosphere and in the common solvents and all solvents were purified and dried according to standard procedures.71 The complexes [Pt(dfppy)(dfppyH)Cl]66 and [Pt(dfppy)(dmso)Cl], A,67 were prepared as published methods. The NMR labeling is shown in Scheme 1 for clarifying the chemical shift assignments.
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7

Phytochemical Analysis of Natural Compounds

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Silica gel H was purchased from Sigma-Aldrich, whereas silica gel 60 (230˗400 mesh), dimetylsulfoxide (DMSO), methanol (MeOH), ethanol (EtOH), n-hexane and ethyl acetate (EtOAc) were purchased from Merck Co. (Germany). 3-(4,5-Dimethylthiazol-2yl)-2, 5-diphenyl tetrazolium bromide (MTT reagent) was provided by Invitrogen (Carlsbad, USA). RPMI-1640 medium (pH 7.4), penicillin/streptomycin and fetal bovine serum (FBS) were purchased from Nacalai Tesque (Japan) and Trypsin-EDTA 10X was supplied by Biowest (USA). The ultraviolet (UV) spectra and the Infrared (IR) spectra were recorded on a UV spectrophotometer (UV-1601 Shimadzu, Japan) and the FT-IR spectrometer Spectrum RXI (Perkin Elmer, USA), respectively. The nuclear magnetic resonance (NMR) spectra were recorded on a 600 MHz Bruker (Switzerland) spectrometer. Optical rotation was performed in Jusco (Tokyo, Japan). Mass spectra were recorded for electron spray ionization (ESI) mass spectrometry on IT-TOF from Shimadzu, Japan. High-performance liquid chromatography (HPLC) analysis was also conducted.
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8

Quantitative LC-MS Analysis of Peptides

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The LC-MS analysis of the peptides was performed on a Shimadzu LCMS-8050 equipped with a triple quadrupole mass spectrometer (using a UHPLC Nexera X2 system) and on an Agilent 6470 Triple Quadrupole LC/MS System equipped with a standard Jet Stream ESI source and Agilent Technologies 1290 Infinity II system. The LC-MS analysis on both instruments were carried out in SIM (selected ion monitoring) mode and with a Q1Q3 scan. The LC system was operated with a mobile phase consisting of solvent A: 0.1% formic acid in H2O and solvent B: 0.1% formic acid in MeCN. The gradient conditions (B %) were from 5 to 80% B, within 15 min. The flow rate was 0.2 mL/min, and the injection volume 5 μL. The separation was performed on an Aeris Peptide XB-C18 column (50 mm × 2.1 mm) with a 3.6 μm bead diameter. The peptide samples were dissolved in 400 μl of a water: acetonitrile mixture (80: 20). Most analysis were carried out on a Shimadzu IT-TOF, which is a hybrid system consisting of an ion trap and a time-of-flight mass analyzer; it also includes an electrospray (ESI) ion source. In our experiments, we set the potential between the spray needle and the orifice to 4.5 kV. The LC separation on this instrument was performed in the same condition as described above.
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9

Quantitative Analysis of Leaf Metabolites

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Ground leaf tissue was weighed and collected into 200 µl methanol containing 40 µM caffeine or 10 µM esculin as an internal standard and incubated at 60 °C for 2 hours. After a 30 minute centrifugation step at 5000 g, an aliquot of the supernatant (25 µl) was mixed with an equal volume of water and analyzed on a Thermo-Finnigan instrument equipped with a Deca XP ion trap detector or a Shimadzu IT-TOF. In both systems the column used was a Phenomenex Kinetic 5 µ C18 100A (100 x 2.10 mm x 5 µm) and the binary solvent system consisted of acetonitrile (ACN) and 0.1% formic acid in water. The elution program was as follows: 1 minute isocratic at 12% ACN, 3.5 minute gradient up to 25% ACN, 2.5 minute gradient up to 50% ACN, 1 minute gradient up to 100% ACN, 6 minute isocratic at 100% ACN, 1 minute gradient down to 12% ACN, and 2.5 minute isocratic at 12% ACN. Peak areas were calculated using the ICIS algorithm in Finnigan’s Xcalibur software or LCMS solutions and normalized by leaf mass (fresh weight) and the peak area of the internal standard.
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10

Luminescent Platinum(II) Complexes: Synthesis and Spectroscopic Analysis

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1H (700 MHz), 13C{1H} (176 MHz),
19F (376 MHz), 31P{1H} (162 MHz) and
195Pt{1H} (64 MHz) NMR spectra were recorded on Bruker
Avance 700, 400 or 300 MHz instruments at room temperature. All chemical shifts
(δ) are reported in ppm relative to their corresponding external
standards (SiMe4 for 1H and 13C{1H},
CFCl3 for 19F, 85% H3PO4 for
31P{1H}, Na2PtCl6 for
195Pt{1H}). The instrument for HR ESI-Mass measurement
was a Shimadzu IT-TOF with an electrospray ionization source, which is part of
the Arkansas Statewide Mass Spectrometry Facility. UV-vis absorption spectra
were recorded on a JASCO V-770 UV-visible/NIR spectrophotometer. Emission
spectra were measured on a JASCO FP-8500 spectrofluorometer. The lifetimes were
measured in the phosphorimeter mode and the quantum yields of the complexes were
measured using an integrating sphere. The 2-phenylpyridine (ppy),
triphenylphosphine (PPh3), silver fluoride (AgF) and all the other
chemicals were purchased from commercial resources. All the reactions were
carried out under Argon atmosphere and in the common solvents and all solvents
were purified and dried according to standard procedures before using.54 The complexes
[Pt(ppy)(PPh3)Cl], 1a, [Pt(ppy)(PPh3)Br],
1b, [Pt(ppy)(PPh3)I], 1c, were prepared
as published methods.42 The
NMR labeling is shown in Scheme 1 for
clarifying the chemical shift assignments.
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