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16 protocols using apollo 2

1

ESI-MS Identification Protocol

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The ESI source (Apollo II, Bruker Daltonics) was used in both negative- and positive-ion modes. The methanolic solutions were infused with a flow rate of 120 µL/h. The drying gas temperature and the flow rate were kept at 180 °C and 4 L/min, respectively, and the pressure of the nebulizer gas was 2.2 bar. In negative detection mode, the capillary voltage was set at 4 kV and while, in positive-ion mode, it was maintained at 3.6 kV. The negative-ion mass spectrum ranges from m/z 147 to 2000 and results from the accumulation of 5000 scans. For positive-ion mode experiment, 3000 scans were accumulated and the mass spectrum ranges from m/z 92 to 1500.
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2

Spectroscopic Characterization of Compounds

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1D NMR and 2D NMR spectra were recorded on a Bruker DRX-400 instrument. HRESIMS was carried out on Bruker Daltonics Apex ultra 7.0 T Fourier transform mass spectrometer with an electrospray ionization source (Apollo II, Bruker Daltonics, Bremen, Germany). Optical rotations were measured with a P-1020 digital polarimeter (JASCO Corporation, Tokyo, Japan). CD spectra were measured on a J-715 spectropolarimeter (JASCO Corporation). The UV spectra were recorded on a UV-1800 spectrophotometer (Shimadzu, Japan). Thin-layer chromatography (TLC) plates (5 × 10 cm) were performed on GF254 (Branch of Qingdao Marine Chemical Co. Ltd., Qingdao, China) plates. For column chromatography (CC), RP-C18 (ODS-A, 50 µm, YMC, Kyoto, Japan), silica gel (200–300 mesh, 300–400 mesh, Branch of Qingdao Marine Chemical Co. Ltd., Qingdao, China), and Sephadex LH-20 (GE Healthcare Bio-Science AB, Pittsburgh, PA, USA) were used. The high performance liquid chromatography (HPLC) analysis was performed on a Waters 2695–2998 system (Waters, Milford, CT, USA). Semi-preparative HPLC was run with a P3000 pump (CXTH, Beijing, China) and a UV3000 ultraviolet-visible detector (CXTH, Beijing, China), using a preparative RP-C18 column (5 µm, 20 × 250 mm, YMC, Kyoto, Japan).
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3

High-Resolution FT-ICR Mass Spectrometry

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Mass spectra were obtained
with an FT-ICR mass spectrometer equipped with a dynamically harmonized
analyzer cell (solariX XR, Bruker Daltonics, Billerica, U.S.A.) and
a 12 T refrigerated, actively shielded superconducting magnet (Bruker
Biospin, Wissembourg, France). The data were acquired in negative
ion mode with an ESI source (Apollo II, Bruker Daltonics, Billerica,
U.S.A., capillary voltage: 4.3 kV) in full profile magnitude mode
with a transient size of 4 MWord (∼1.6 s free induction decay,
FID). The ion accumulation time (IAT) was set to 1.6 s, and the mass
range was set to m/z 147–1000.
The mass resolving power (m/Δm, full width half-maximum) at m/z 400 was approximately 500,000 ±
40,000, which is sufficient to resolve all major DOM ions in the considered
mass range. SRFA spiked with model compounds was measured with 0.5
s IAT (cf. SI Text: Instrument Quality Control).
As reference to state-of-the art analysis, the PPL extracted
seawater sample (AOhighSPE) was diluted to 0.8
mmol DOC L–1 (10 mg DOC L–1) in
ultrapure water and MeOH (50/50, v/v) and measured with the standard
direct infusion (DI-) FT-ICR MS method (256 scans, 4 MWord, 8 ms IAT,
ESI(−), 4 μL min–1).
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4

Omics Analyses Using UHPLC-Q-TOF

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Omics analyses were performed on a Thermo Ultimate UHPLC system (Thermo Scientific, Bremen, Germany) coupled online to a TimsTOF Pro Quadrupole Time of Flight (Q-TOF) (Bruker Daltonics, Bremen, Germany) equipped with an Apollo II electrospray ionization (ESI) probe. Detailed instrument parameters are reported in Additional file 1: Section S.1.
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5

Chitobiose Analysis by QTOF-MS

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Chitobiose obtained from quantitative HPLC was further analyzed by quadrupole-time‐of‐flight‐mass spectrometry (QTOF-MS) (Bruker Biospin AG, Bangkok, Thailand). Chitobiose dissolved in water (2 mg.mL−1, 100 μL) was injected into the instrument. A mass range of 50–1000 was selected for data acquisition. Positive ionization mode was chosen using source type Electrospray Ionization (Bruker Apollo II, Thailand). The capillary and charging voltage were set at 4500 V and 2000 V, respectively.
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6

Optimized Electrospray Ionization Source

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An orthogonal, commercial ESI source based on the Apollo II design (Bruker Daltonics, Inc., MA) was used. Briefly, sample solutions were introduced into the nebulizer at a rate of 120–180 μL/min using an external syringe pump. Typical operating conditions were 4000–4500 V capillary voltage, 600 V endcap capillary offset voltage, 10 L/min dry gas flow rate, 1.0 bar nebulizer gas pressure, and a dry gas temperature 180 °C. Ions from the ESI source are introduced via a 0.6 mm inner diameter, single-bore glass capillary tube, which is resistively coated across its length, allowing the nebulizer to be maintained at ground potential, while the capillary exit was biased to around 180V.
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7

Ultra-High Resolution FT-ICR-MS for Plant Metabolite Analysis

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Ultra-high resolution mass spectra were acquired using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer (Solarix, Bruker) with a 12 Tesla superconducting magnet (Magnex Scientific Varian Inc.). Samples dissolved in 70% MeOH were ionized by electrospray ionization (ESI, Apollo II; Bruker Daltonics) at a flow rate of 2 μl min–1. The temperature of the dry gas (N2) was 200 °C at a flow of 2 litres min–1. Mass spectra were recorded in a scan range of 128–1000 m/z with an ion accumulation time of 300ms. A total of 300 scans were accumulated for each MS acquisition. The FT-ICR-MS spectra were normalized by using the exact masses of known plant metabolites including C16 and C18 fatty acids with the Bruker Daltonics data analysis software. For linearization, absolute signal intensities were divided by the maximum amplitude of noise, yielding signal-to-noise (S/N) ratios.
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8

Metabolic Profiling by FT-ICR-MS

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Prior to FT-ICR-MS analyses, a PPE was performed following the protocol of Willkommen et al. (2018a) (link). The measurement of metabolic features was acquired by means of FT-ICR-MS (Solarix, Bruker, Bremen, Germany), equipped with a 12-T superconducting magnet (Magnex Scientific, Varian Inc., Oxford, United Kingdom) and an ESI source (Apollo II, Bruker Daltonics, Bremen, Germany) as shown in the detailed description in Willkommen et al. (2018a) (link).
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9

Tryptic Peptide Analysis by LC-MS/MS

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Tryptic peptides were analyzed using a Dionex 3000RS LC system (Thermo Fisher Scientific) coupled on-line to a Bruker Impact II QTOF mass spectrometer equipped with an Apollo II ion source (Bruker Daltonics, Solna, Sweden). The peptides (80 μg) were loaded onto an Aeris Peptide column (2.6 μm, xb-C18, 250 × 2.1 mm, Phenomex, Værløse, Denmark), and separated by reverse-phase chromatography with a multi-step gradient of 5–45% buffer B (80% acetonitrile (ACN), 3% DMSO and 0.1% formic acid (FA)) mixed with buffer A (3% DMSO and 0.1% FA) at a flow rate of 200 μL min−1 over 120 min, followed by washing and re-equilibration steps (total run time: 150 min). LC-MS/MS data were acquired using a data-dependent method. A high resolution TOF-MS scan over a mass range of 150–2200 m/z, was followed by MS/MS scans of top 20 most intense precursor ions per cycle. Dynamic exclusion of precursor ions was set to 30 s duration after acquisition of 3 spectra, with a window of 0.05 Th. Acquisition rate was set to 4 Hz (MS) and 2–16 Hz (MS/MS, adjusted by precursor ion intensity).
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10

High-Precision Mass Spectrometry Characterization

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Individual standards were analyzed using high resolution mass spectrometry to confirm the purity of the samples. High resolution mass spectrometry analysis was performed in a Solarix 7T FTICR-MS from Bruker Daltonics Inc. (Billerica, MA). An atmospheric pressure photo ionization source (APPI, based on the Apollo II design, Bruker Daltonics Inc., MA) using a Kr lamp with main emission bands at 10.0 and 10.6 eV was used for all analyses. All standards were observed with sub ppm mass accuracy.
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