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10 protocols using 1260 infinity liquid chromatography system

1

SEC-MALS Analysis of PML RING Mutants

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The purified PML RING1–119 and mutants were subjected to gel filtration analysis (S100 column, GE Healthcare). The elution peaks, as monitored by UV absorption at 280 nm, were pooled separately and chosen for size exclusion chromatography-multi-angle light scattering (SEC-MALS) characterization, respectively. In brief, the purified protein samples were concentrated and analyzed using a WTC-015S5 sized exclusion column (Wyatt Technology) which was connected to a 1260 infinity liquid chromatography system (Agilent Technology) equipped with inline DAWN HELEOS-II MALS and Optilab rEX differential refractive index detectors (Wyatt Technology). For each sample, a 40 μl injection volume and 0.5 ml min−1 flow rate were applied. Data were recorded and processed using ASTRA VI software (Wyatt Technology).
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2

Gel Filtration Analysis of SafDAA-dsc and Mutants

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SafDAA-dsc and mutants were subjected to gel filtration analysis using a WTC-015S5 sized exclusion column (Wyatt Technology). The elution of each sample was analyzed by a 1260 infinity liquid chromatography system (Agilent Technology) linked with inline DAWN HELEOS-II MALS and Optilab rEX differential refractive index detectors (Wyatt Technology). For each run, a 40-μl sample (2.5 mg/ml) was injected. The sample was eluted at a flow-rate of 0.5 ml/min for SafDAA-dsc and mutants. Data were recorded and analyzed using ASTRA VI software (Wyatt Technology).
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3

High-pH Reverse-Phase HPLC Peptide Fractionation

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Agilent 1260 Infinity Liquid Chromatography System was used at 35˚C. High-pH reverse-phase HPLC was performed to separate the peptides using an Agilent 300 Extend C18 column (Agilent Technologies, Inc.). The column size was ZORBAX Extend-C18 Agilent Analytical 4.6x250-mm 5-Micron 80A. The composition of mobile phase (two solvents) were: Buffer A, 98% water and 2% acetonitrile; buffer B, 98% acetonitrile and 2% water. The flow rate was used at 1 ml/min. Briefly, the peptides were fractionated into 60 fractions with acetonitrile (8-32%) at pH 9 for 60 min. The sample quantity was 1,000 µl. Pre-loading: Dried sample dissolved in buffer A, and then centrifuged at 18,000 x g for 5 min. Sample combination method: The samples were collected from the 11th min to the 64th min when they flowed out of the liquid phase, and then the first component were combined with the 11th, 29th, 47th and 64th min samples.
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4

Quantitative Analysis of Phytochemical Profiles

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The phytochemical compositions of the extracts were analyzed quantitatively. Quantitative analyzes were carried out by using LC–ESI–MS/MS technique (Agilent Technologies 1260 Infinity liquid chromatography system, Santa Clara, CA, USA) [70 (link)]. Information on the details of the performed analyzes are included in the Supplementary File (Tables S1 and S2). All tests were carried out in triplicate. In order to determine the degree of statistical difference, Tukey’s test was used.
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5

Glutamylated Peptide Purification and Deglutamylation

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The glutamylated precursor peptide NisA was incubated with endoprotease ArgC under the following conditions: glutamylated NisA (500 µM), Tris-HCl (20 mM), CaCl2 (10 mM), EDTA (0.5 mM), DTT (5 mM), and ArgC (0.005 µg µL−1). The reaction was incubated for 4 h at 37 °C. Glutamylated core and leader peptide were purified by analytical high performance liquid chromatography (HPLC) on a Phenomenex C18 column (Luna, 250 mm × 4.60 mm, 10 µ, 100 Å) connected to an Agilent 1260 infinity liquid chromatography system. Peptides were separated using a linear gradient of 2% (v/v) Solvent B (80% (v/v) Acetonitrile (MeCN), 20% (v/v) H2O, 0.086% (v/v) trifluoroacetic acid (TFA)) in Solvent A (0.1% (v/v) TFA in H2O) to 100% (v/v) Solvent B over 60 min at a flow rate of 1 mL min−1. Peptide elution was monitored using a 220 nm wavelength. Desired fractions were lyophilized and stored at −20 °C.
The following reaction conditions were used for the glutamate elimination assays: HEPES pH 7.5 (100 mM), glutamylated His6-NisA core peptide (~ 100 µM), NisB (5 µM), MgCl2 (10 mM), KCl (10 mM), and TCEP (1 mM). The reaction was performed in a 15 µL volume, incubated for 60 min at 30 °C and analyzed by MALDI-TOF MS as described above.
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6

Quantitative Analysis of Isomeric Compounds

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An Agilent Technologies 1260 Infinity liquid chromatography system coupled to a 6420 Triple Quadrupole mass spectrometer was used for the qualitative and quantitative analyses. The separation was achieved by means of a Poroshell 120 EC-C18 (100 mm × 4.6 mm I.D., 2.7 μm) column, and using 0.1% formic acid (A)/methanol (B) as mobile (selected based on the sufficient chromatographic resolution of isomeric compounds). This configuration also allows for improvements in the method sensitivity. The gradient elution profile herein adopted was set as follows: 0.00 min 2% B eluent, 3.00 min 2% B eluent, 6.00 min 25% B eluent, 10.00 min 50% B eluent, 14.00 min 95% B eluent, 17.00 min 95% B, and 17.50 min 2% B eluent. The column temperature was maintained at 25 °C. The flow rate was 0.4 mL/min, and the injection volume was 2.0 μL. The MS instrumentation was directly coupled with the LC system via an ESI source, operating both in negative and positive multiple reaction monitoring (MRM) mode. The ESI parameters were: capillary voltage −3.5 kV, gas temperature 300 °C, gas flow 11 mL/min, nebulizer pressure 40 psi.
The different analytes were identified by means of their retention times, mass spectra, and tandem mass spectra. Specifically, quantitative analyses were performed using a specific MRM transition for each analyte.
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7

Photoelectrochemical Biocatalysis and NADH Regeneration

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Photoelectrochemical biocatalysis was coupled with the photoelectrochemical regeneration of NADH using the FeOOH/BiVO4/perovskite solar cell tandem configuration with the two-electrode configuration. The reaction medium for the enzymatic reaction consisted of NAD+ (2 mM), M (0.5 mM), α-ketoglutaric acid disodium salt dihydrate (50 mM), (NH4)2SO4 (250 mM), and GDH (40 U) in 3 ml of phosphate buffer (0.1 M, pH 7.5). The l-glutamate production was analyzed by using a 1260 Infinity liquid chromatography system (Agilent Technologies, U.S.A.). TTNGDH, TOFGDH were calculated according to Eqs. (2) and (3), respectively: TTNGDH=MaximumconcentrationofL-glutamateConcentrationofGDH, TOFGDHh-1=ConcentrationofL-glutamateafterreactionforthefirsthourConcentrationofGDH×time.
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8

Tacrolimus Fiber Release Kinetics

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To assess release kinetics, 10.0 ± 0.1 mg of random tacrolimus fibers (n = 3 separate fiber mats, three sections per mat) and 10.0 ± 0.2 mg of aligned tacrolimus fibers (n = 3 separate fiber mats, one section per mat) were incubated with 1 ml release buffer (50 mM NH 4 HCO 3 ± 0.02% NaN 3 ) in microtubes in an Incu-shake MINI shaking incubator (SciQuip, UK) set at 37°C and 75 RPM. Release buffer was exchanged every 2-3 days and then stored at -20°C prior to determination of tacrolimus content. Liquid chromatography-mass spectrometry was used to detect tacrolimus released from fibers, as reported previously [Citation37] . Briefly, a 1260 Infinity liquid chromatography system (Agilent, UK) coupled to a 6460 triple quadrupole mass spectrometer (Agilent) was used with an Agilent Pursuit 5 μm C8 50 × 2.1 mm column and gradient elution of water and methanol mobile phases, buffered with 10 mM ammonium formate and 0.05% formic acid. A validated protocol was used as the basis for analysis [Citation38] .
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9

Isolation and Purification of Acyl-HSL from M. fujisawaense

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An exponentially growing culture of M. fujisawaense DSM5686 was used to inoculate one L modified AMS + 50 mM MeOH to a starting optical density of 0.02. A total of 6 1 L cultures were grown at a time. These cultures were incubated at 30°C and shaken at 200 rpm to stationary phase (approximately 72 hours). The culture was centrifuged at 4,700 rpm for 10 min followed by extraction of the clarified supernatant with an equal volume of ethyl acetate acidified with 0.01% (vol/vol) acetic acid. The organic phase was then dried by rotary evaporation. Dried crude supernatant extracts were resuspended in 1 mL of 1:3 water:acetonitrile (ACN) and applied onto a preequilibrated Discovery C18 solid-phase extraction (SPE) column (3 mL, 500 mg) then washed and eluted sequentially with 6 mL of 25%, 50%, 75%, and 100% ACN in water. The acyl-HSL was found in the 75% ACN fraction by LC-MS. This fraction was dried and resuspended in 500 µL of 25% ACN in water and separated using an Agilent 1260 Infinity liquid chromatography system. A Waters SunFire C18 column (3.5 µm particle size, 46 mm × 100 mm) was used for reverse phase separation with a flow rate of 1 mL min−1. Solvent A: Water + 0.1% trifluoroacetic acid; Solvent B: ACN + 0.1% trifluoroacetic acid. Gradient: 0–1 min, 10–35% B. 1–21 min, 35–55% B. 21–22 min, 55–100% B. 22–30 min, 100% B. 30–31 min, 100–10% B. 31–36 min, 10% B.
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10

Lipidomic Analysis of Purified Hepatocyte Nuclei

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Primary hepatocytes isolated as described above were resuspended in hypotonic lysis buffer (10 mM Hepes, 5 mM MgCl2, 10 mM NaCl, pH 7.4) containing proteinase inhibitor cocktail (Sigma-Aldrich) and incubated on a rotating wheel for 30 min at 4°C. To isolate nuclei, the cell lysates were homogenized with a Wheaton Dounce homogenizer (DWK Life Sciences), underlaid with a 40% sucrose cushion, and centrifuged at 800 g for 20 min. Fractionation was verified by immunoblotting using Abs against the nuclear proteins lamin A/C (Santa Cruz Biotechnology, sc-20681) at a dilution of 1:1,000 and the cytoplasmic protein GAPDH (Thermo Fisher Scientific, AM4300) at a dilution of 1:5,000). Lipidomic analysis of purified nuclei was performed at the Columbia University Biomarker Core Laboratory using an LC-MS/MS platform comprised of a 6490 Triple Quadrupole mass spectrometer integrated with a 1260 Infinity liquid chromatography system (Agilent Technologies).
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