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12 protocols using esquire 3000 plus iontrap mass spectrometer

1

Irradiation Effects on 7-DHC and Lipids

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7-DHC and DHCEO samples were prepared by dissolving the compounds in a mixed solvent containing 4:1 CH3CN and Mil-Q-H2O. Samples received ionizing radiation (IR, 320 KV, 5 Gy), and analyzed after 24 h. For comparison, samples containing 7-DHC and 20% H2O2 were also tested. 16:0-18:2 PC/7-DHC samples were prepared by dissolving 16:0-18:2 PC and 7-DHC at a 3:1 molar ratio in a 2:1 v/v of CHCl3:MeOH solution. After removing the solvent by rotovap, 16:0-18:2 PC/7-DHC was resuspended in 1 mL Mil-Q-H2O. Liquid chromatography was performed on an Applied Biosystems 140 B solvent delivery system using water with 0.1% formic acid as solvent A and acetonitrile as solvent B. The linear solvent gradient was from 70% B to 95% B over 20 minutes at a flow rate of 50 μL/min. A Thermo Hypersil-Keystone 1 x 150 mm Biobasic-4 column with 5 μm particle size and 300A pore size was used. The effluent was directed into a Bruker Daltonics Esquire 3000 plus ion trap mass spectrometer equipped with an atmospheric pressure chemical ionization (electrospray ionization for the lipid sample) source. The dry as temperature was held at 300 degrees C at a flow rate of 4 L/min nitrogen. The nebulizer was set to 15 PSI of nitrogen. The vaporizer temperature was held at 380 degrees C.
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2

Mass Spectrometry Analysis of Microalgal Compound

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To determine the molecular weight of the isolated compound and to confirm peak purity HPLC–MS experiments were performed, using a 1100 HPLC system from Agilent (Agilent), coupled to an Esquire 3000 plus iontrap mass spectrometer (Bruker, Bremen, Germany). MS-Spectra were obtained applying alternating ESI mode and by setting the temperature to 350 °C, the nebulizer gas (nitrogen) to 40 psi, and a nebulizer flow (nitrogen) of 8 L min−1. Additionally, the exact mass of the compound was determined by analysing the sample on a micrOTOF-Q II MS (Bruker). Here the settings were: nebulizer gas, 5.8 psi (nitrogen); dry gas, 4.0 L min−1 (nitrogen); and dry temperature, 180 °C. Capillary voltage was 4.0 kV (positive ESI mode). The scanned mass range was between m/z 50 and 500 (Fig. 3).

HPLC–MS data for molecular weight determination of the novel MAA in the terrestrial green alga Prasiola calophylla. Top HPLC chromatogram of the purified Prasiola extract. Middle and below Extracted ion chromatogram (EIC) and mass spectrum of the purified MAA, corresponding to an m/z value of [M+H]+, respectively

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3

Molecular Weight Determination of Isolated Compound

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To determine the molecular weight of the isolated compound and to confirm peak purity HPLC–MS experiments were performed, using a 1100 HPLC system from Agilent (Agilent), coupled to an Esquire 3000 plus iontrap mass spectrometer (Bruker, Bremen, Germany). MS-Spectra were obtained applying alternating ESI mode and by setting the temperature to 350 °C, the nebulizer gas (nitrogen) to 40 psi, and a nebulizer flow (nitrogen) of 8 L min−1. Additionally, the exact mass of the compound was determined by analysing the sample on a micrOTOF-Q II MS (Bruker). Here the settings were: nebulizer gas, 5.8 psi (nitrogen); dry gas, 4.0 L min−1 (nitrogen); and dry temperature, 180 °C. Capillary voltage was 4.0 kV (positive ESI mode). The scanned mass range was between m/z 50 and 500 (Fig. 3).
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4

HPLC Purification and Characterization of Polyphenols

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Quercetin (12, >98%) was purchased from Sigma-Aldrich. Gallic acid (1, >98%), hyperoside (8, >95%), isoquercitrin (10, >95%), and polyamide (particle size: 0.05–0.16 mm) were from Carl Roth. HPLC-grade acetonitrile and methanol (Reuss Chemie AG), and distilled water were used for HPLC separations.
Preparative HPLC was carried out on an LC 8A preparative liquid chromatograph equipped with a SPD-M10A VP PDA detector (all Shimadzu). A SunFire C18 column (150 × 30 mm i.d., 5 μm; Waters) connected to a pre-column (10 × 10 mm) was used, at a flow rate of 20 mL/min. HPLC-based activity profiling was performed on an Agilent 1100 system equipped with a PDA detector. A SunFire C18 column (150 × 10 mm i.d., 5 μm; Waters) connected to a pre-column (10 × 10 mm) was used. The flow rate was 4 mL/min. Time-based fractions were collected with a Gilson FC204 fraction collector. ESI-MS spectra were obtained on an Esquire 3000 Plus ion trap mass spectrometer (Bruker Daltonics). NMR spectra were recorded on an Avance III 500 MHz spectrometer (Bruker BioSpin) equipped with a 1-mm TXI microprobe.
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5

Mass Spectrometry Analysis of Betanin

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Mass spectrometry was performed as described by Gonçalves et al. [17 (link)]. The RP-HPLC purified fraction was ionized in the positive mode and ions were monitored in the full scan mode (range of m/z 50–1500). The ESI(+)-MS/MS analysis was carried out on a Bruker Esquire 3000 Plus Ion Trap Mass Spectrometer (Bruker Co., Billerica, MA, USA) equipped with an electrospray source in the positive ion mode. Nitrogen was used as the nebulizing (45 psi) and drying gas (6 L∙min−1, 300 °C) and helium as the buffer gas (4 × 10−6 mbar). The high capillary voltage was set to 3500 V. To avoid space–charge effects, smart ion charge control (ICC) was set to an arbitrary value of 50.000. Betanin identification was based on its mass (550 g∙mol−1) and by similarity with the commercial standard and literature-available spectra [39 (link)].
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6

HPLC-MS/MS Analysis of Compounds

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A Bruker Daltonics esquire 3000 plus ion trap mass spectrometer (Bruker Daltonics, Bremen, Germany) connected to an Agilent 1100 HPLC system (Agilent Technologies, Waldbronn, Germany) and equipped with a quaternary pump and a variable wavelength detector was utilized for all experiments. Components were separated with a Phenomenex (Aschaffenburg, Germany) Luna C-18 column (150 mm long × 2.0 mm inner diameter, particle size 5 μm) that was held at 25 °C. The electrospray ionization voltage of the capillary was set to −4000 V and the end plate to −500 V. Nitrogen was used as dry gas at a temperature of 300 °C and a flow rate of 10 l/min. The full scan mass spectra were measured in a scan range from 50 to 800 m/z with a scan resolution of 13000 m/z/s until the ICC target reached 20,000 or 200 ms, whichever was achieved first. Tandem mass spectrometry was carried out using helium as the collision gas (3.56 × 10–6 mbar) with the collision voltage set at 1 V. Spectra were acquired in the positive and negative ionization mode. The LC parameters went from 100% A (0.1% formic acid in water) to 50% B (0.1% formic acid in methanol) in 30 min, then in 5 min to 100% B, held for 15 min at these conditions, then returned to 100% A in 5 min at a flow rate of 0.2 ml min−1. The detection wavelength was 280 nm.
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7

Molecular Mass Analysis of FBuOH Fractions

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This analysis was performed to determine the molecular masses of positive ions detected and to identify the components present in FBuOH and its sub-fractions. The analyses were conducted using a 10AD-VP chromatographic system coupled with a Shimadzu SPD-M10AVP DAD detector (Shimadzu, Kyoto, Japan) and an Esquire 3,000 Plus-Ion Trap mass spectrometer (Bruker Daltonics, GmbH, Bremen, Germany) equipped with a 4,000 V capillary, a nebulizer set at 27 psi, a drying gas flux of 7 l/min, and a temperature of 320°C, in positive ion mode.
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8

Synthesis and Purification of Compound 1

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All reagents and solvents
were reagent grade and used as purchased from commercial sources.
Compound 1 was synthesized at the Institute of Inorganic
Chemistry, University of Vienna. The purity of the used batch of 1 was checked at the Microanalytical Laboratory of the University
of Vienna by both elemental analysis applying a PerkinElmer 2400 CHN
elemental analyzer and mass spectroscopy applying a Bruker Esquire
3000 Plus Ion Trap mass spectrometer. The results revealed a deviation
of ±0.9 and ±0.1%, respectively, from the calculated value,
thus confirming ≥95% purity for 1.
Protein
purification was performed by size-exclusion chromatography (SEC)
using the ÄKTA explorer system from GE Healthcare. The purity
of the protein samples was checked by SDS-PAGE using a 15% acrylamide-containing
gel and the Mini-PROTEAN Tetra Cell from Bio-Rad. For highly concentrated
protein samples (75–120 mg/mL) to be obtained, ultrafiltration
was performed using Vivaspin concentrators with a 30 kDa cutoff membrane
from Sartorius. For the determination of protein concentrations, the
protein’s absorbance at 280 nm was measured by UV–vis
spectroscopy (UV-1800 from Shimadzu), and the concentrations were
subsequently calculated applying the Beer–Lambert Law using
the molar extinction coefficient (at 280 nm) of 36500 M–1 cm–1 for HSA.74 (link)
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9

Fruit Firmness and Metabolite Analysis

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The firmness was measured using a texture analyser (TA.XT2i; Stable Micro Systems, https://www.stablemicrosystems.com) fitted with a 5‐mm flat probe. Each fruit was penetrated to 5 mm in depth at a speed rate of 0.5 mm sec−1 and the maximum force developed during the test was recorded in Newton (N). Each fruit was measured twice at opposite sides of its equatorial zone. LC‐MS was performed using an Agilent 1100 HPLC/UV system (Agilent Technologies, https://www.agilent.com) with a reverse‐phase column (Luna 3u C18(2) 100A, 150 × 2 mm; Phenomenex, https://www.phenomenex.com) and connected to a Bruker esquire3000plus ion‐trap mass spectrometer (Bruker, https://www.bruker.com). LC‐MS analysis was performed according to the protocol described by Ring et al. (2013 (link)). The values were expressed as per mil (‰) equivalent internal standard per dry weight using biochanin as internal standard.
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10

HPLC/MS Quantification of Secondary Metabolites

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Levels of secondary metabolites were determined on an Agilent 1100 HPLC/UV system (Agilent Technologies, Germany) equipped with a reverse-phase column (Luna 3 u C18(2) 100 A, 150 × 2 mm; Phenomenex, Germany), a quaternary pump, and a variable wavelength detector. Connected to the HPLC was a Bruker esquire3000plus ion-trap mass spectrometer (Bruker Daltonics, Germany). HPLC and mass spectrometry were performed at optimized conditions33 (link)95 (link). Resulting data were analyzed with Data Analysis 5.1 software (Bruker Daltonics, Germany), and metabolites were identified using the in-house database. Levels (per mil equivalents of the dry weight, ‰ equ. dw.) of secondary metabolites quantified during targeted analyses are summarized in Supplementary Tables S4 and S5.
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