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31 protocols using api 2000

1

Quantitative Analysis of Amniotic Fluid Biomarkers

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The levels of C5 and C2 were quantitatively analyzed by MS/MS (Applied Biosystems, API 2000) using 3 μl of AF supernatant and the levels automatically calculated based on the assigned values for internal standards using Chemo View v1.2 software (Han et al., 2007 (link)). (Parameters for MS/MS analysis are listed in Supplementary Table S1) The organic acid fraction was extracted, methylated, and analyzed by chemical ionization GC/MS (QP 2010, Shimadzu Limited, Kyoto, Japan) operated in selected ion monitoring mode. For each AF supernatant sample, 2 ml of sample was mixed with stable isotope-labeled compounds and internal standards as described by Hasegawa et al. (2005) (link). Concentrations of IVG in the AF were calculated using GC-MS Solution v2.40 software. (Parameters for GC/MS analysis are listed in Supplementary Table S2.) Standard scatter plots were generated for level of C5, C5/C2 and IVG in affected and unaffected groups using Prism 8 (Graph-Pad Software Inc.).
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2

Novel DNA Synthesis and Characterization

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Chemicals and anhydrous solvents were purchased from Fluka-Sigma-Aldrich. TLCs were run on Merck silica gel 60 F254 plates. Silica gel chromatography was performed using Merck silica gel 60 (0.063–0.200 mm). The API 2000 (Applied Biosystems) mass spectrometer was used to perform the analyses of the intermediates and the monomer. NMR data were collected on Varian Mercury Plus400 and UNITYINOVA 500 MHz spectrometers equipped with a broadband inverse probe with z-field gradient, and on a Varian UNITYINOVA 700 MHz spectrometer equipped with a triple resonance cryoprobe. The data were processed using the Varian VNMR and the iNMR (http://www.inmr.net) software packages. Reagents and phosphoramidites for DNA syntheses were purchased from Glenn Research. ON syntheses were performed on a PerSeptive Biosystem Expedite DNA synthesizer. HPLC purifications and analyses were carried out using a JASCO PU-2089 Plus HPLC pump equipped with a JASCO BS-997–01 UV detector. CD experiments were performed on a JASCO 715 spectropolarimeter equipped with a PTC-348 temperature controller. The fibrinogen assay was performed using a JASCO 530 UV spectrophotometer equipped with the PTC-348 temperature controller.
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3

Confirming Homo-Polymerization via MS/MS

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Electrospray ionization‐mass spectrometry coupled with CID (Collision‐induced dissociation) MS/MS (API 2000; Applied Biosystems Foster City, CA, USA) was performed in negative mode (−4000 V) to confirm whether the 2,7‐DHN underwent homo‐polymerization to form the material‐independent coating. Deionized water was used to prepare the reaction solutions in order to prevent salts from causing inaccuracies in the m/z measurements. After 24 h of reaction, 0.5 ml of each sample was filtered through a 0.45 μm syringe filter (Millipore PTFE type) and then mixed with 0.5 ml of pure acetonitrile. Before analysing the reaction samples, we first obtained CID MS/MS data for the monomer. We then compared the CID MS/MS fragmentation patterns of homo‐oligomer ions with those of the standard monomer to elucidate the monomer composition of the oligomer ions.
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4

Mass Spectrometric Peptide Analysis

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Mass spectra were acquired using an Applied Biosystems API2000 liquid chromatography/tandem mass spectrometry triple quadrupole mass spectrometer (Applied Biosystems, Carlsbad, CA, USA) equipped with an electrospray ionization source in positive ion mode (m/z 400–1800, with a declustering potential of 10–20 V and 0.1 Da steps). The molecular weight of the peptide was deduced from the multiply charged species using Analyst v1.4 with Bioanalyst extensions (Applied Biosystems).
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5

Sterol Quantification by HPLC-MS

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Serum samples were saponified with ethanolic KOH. A mixture of deuterated cholesterol and ergosterol was used as internal standard. Samples were gassed with nitrogen and hydrolyzed at 37 °C for 3 h. Sterols were extracted twice with 0.5 mL hexane and washed with distilled H2O. The solvent was evaporated and residues solved in hexane:isopropanol (99:1). For determination of cholesterol, desmosterol and lathosterol, sterols were derivatized to picolinyl esters according to the method of Honda et al. [22] (link). Dehydrocholesterol was derivatized with PTAD (4-phenyl-1,2,4-triazole-3,5-dione). The analysis of the cholesterol derivatives was performed by HPLC (Agilent 1100, Agilent Technologies, Waldbronn, Germany), coupled to an MS system (API 2000, Applied Biosystems, Darmstadt, Germany).
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6

HPLC-MS/MS Characterization of Compounds

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Mass spectra were recorded on an API 2000 liquid chromatography-tandem mass spectrometry (LC-MS)/MS spectrometer (electron spray ion source, Applied Biosystems) coupled with an Agilent 1100 HPLC system using a Phenomenex Luna HPLC C18 column (50 × 2.00 mm, particle size 3 μm). Compound purity was determined by HPLC-ultraviolet using the following procedure. A amount of 10 μl of compound (1 mg ml−1 in methanol) was injected and eluted with a gradient of water/methanol containing 2 mM ammonium acetate from 60:40 to 0:100 for 10 min, and subsequently with 0:100 for 10 min at a flow rate of 300 μl min−1, starting the gradient after 10 min. Ultraviolet absorption was detected from 220 to 400 nm using a diode array detector.
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7

Optimizing Mass Spectrometry Conditions

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To optimize MS conditions, a solution containing 100 ng/mL of matrine was infused into the tandem mass spectrometer (API 2000; Applied Biosystems, Foster City, CA, USA) at a flow rate of 10 μL/min. The turbo ion spray interface was operated in positive ion mode at 5500 V for spray voltage and ion spray temperature was set to 350°C. The precursor ions of the analytes were optimized as protonated molecular ions, [M + H]+. Matrine was quantified using the multiple reaction monitoring mode and the peak-area ratio method with an IS.
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8

Glycerol and Metabolite Quantification

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Glycerol concentration was monitored by HPLC analysis. Coculture samples were centrifuged at 12,000g for 2 min to collect cell-free broth, which was then filtered through 0.2-μm-pore-size polytetrafluoroethylene membrane syringe filters (VWR International) before subjected to HPLC analysis. The HPLC system consisted of a Bio-rad HPX-87H column, a Waters 2695 separation module and a Waters 410 differential refractometer. Isocratic elution was conducted using 14 mM sulfuric acid as mobile phase at a flow rate of 0.7 mL/min.
The concentration of MA product and the pathway intermediates were determined by LC/MS/MS analysis. Cell-free broth was collected by 12,000g centrifugation for 5 min followed by filtration through 0.2-μm-pore-size polytetrafluoroethylene membrane syringe filters (VWR International). 10 μL 1 g/L p-coumaric acid internal standard was added into 1 mL of the filtered broth. 10 μL of the mixed solution was then injected into an Applied Biosystems API2000 LC/MS/MS running on a previously established method [20 (link)].
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9

Organic Synthesis Characterization Methods

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Chemicals were purchased from Merck (Darmstadt, Germany), ABCR (Karlsruhe, Germany) or TCI (Eschborn, Germany). Analytical thin layer chromatography (TLC) was performed on TLC plates F254 (Merck) and analyzed using UV light. High resolution mass spectra (HR-MS) were recorded on a micrOTOF-Q mass spectrometer (Bruker), low resolution mass spectra (LR-MS) on an API 2000 (Applied Biosystems) mass spectrometer. 1H NMR and 13C NMR spectra were recorded in CDCl3 or (CD3)2SO on a Bruker Ascend 600 MHz NMR-spectrometer operating at 600.18 MHz (1H), and 150.93 MHz (13C). Chemical shifts (δ) are reported in ppm and are referenced to the chemical shifts of the residual solvent proton(s) present in chloroform δ [(CHCl3) = 7.26 ppm for the 1H NMR spectra and δ (CDCl3) = 77.16 ppm for the 13C NMR spectra] and in dimethylsulfoxide δ ((CH3)2SO) = 2.50 ppm for the 1H NMR spectra and δ ((CD3)2SO) = 39.52 ppm for the 13C NMR spectra. Multiplicity: s, singlet; d, doublet; q, quartet; m, multiplet. Coupling constants (J) are shown in Hertz (Hz). The infrared spectra were recorded as solid samples on an ALPHA-T (Bruker) with a Platinum ATR Module using the Opus software. The IR spectra were measured in the attenuated total reflection (ATR) mode in the region of 4,000–385 cm−1 (s, strong; m, medium; w, weak) and are reported in cm−1.
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10

Dried Blood Spot Amino Acid Analysis

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The amino acids in dried blood pots on filter paper were determined by MS/MS (Applied Biosystems, API 2000). All the chemicals used in MS/MS (methanol, and acetonitrile) were liquid chromatographic/mass purity grade and were purchased from Fisher Scientific. The preparation and detection methods were described in previous studies.19, 20 In brief, dried blood spots were extracted using methanol, which contained amino acids as internal standards. After derivatization with n‐butyl alcohol hydrochloric acid, the samples were tested using MS/MS. A total of 17 amino acids were determined, including Phe, Tyr, alanine (Ala), Asp, Glu, Met, Val, Arg, Gly, Gln, His, Ser, Thr, Leu, Trp, Cit, and Orn.
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