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11 protocols using xb c18

1

Extraction and Identification of Carotenoids from Hungarian Red Pepper

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Hungarian red sweet pepper powder (in 1–5 g) was applied in triplicates to extract carotenoids and extraction was carried out with 50 mL dichloroethane:acetone:methanol as solvent mixture in 2:2:1 ratio. Next, the mixture was mixed in an ultrasonic water bath for 30 min, then filtered through a filter paper (Munktell-292). Afterwards, a 0.22 µm PTFE syringe filter (TPP Techno Plastic Products AG, Trasadingen, Switzerland) was used for further purification. Filtered residue was vaporized at 40 °C at 0.2 bar and then filtrate was solved in an high-performance liquid chromatographic (HPLC) pigment reagent (isopropanol:ACN:methanol in 55:35:10 proportion) (Merck, Darmstadt, Germany) [50 (link)]. A HPLC separation was performed on Phenomenex Kinetex® column (2.6 µm, XB-C18, 100 Å, 100 × 4.6 mm) (Phenomenex, Torrance, CA, USA) with 2 gradient elutions: A: 11% methanol, B: isopropanol:ACN:methanol (55:35:10 V/V/V%) mixture. Gradient elution steps were the following: 0–3 min solvent A 100%; 15–20 min solvent A 20%; 25–45 min solvent B 100%; 48–50 min solvent A 100%. Flow rate was 0.6 mL/min and Diode Array Detector (DAD) detection was carried out on 460 nm and 350 nm. Samples were injected in 10 µL and after DAD detection was applied at 460 nm and 350 nm. HPLC profile is shown in Figure 1. Carotenoid compounds with the greatest areas were identified and involved in Table 1.
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2

Ubiquitin Hydrolysis and Mass Spectrometry

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Ubiquitin pepsine hydrolysate (1 mg, 5.78 × 10−7 mol) was dissolved in 1 mL of triethylammonium bicarbonate (TEAB) buffer (pH 8.4–8.6). The solution was divided into two portions: 0.5 mL was retained as a control sample and the second 0.5 mL was tagged with 1.13 mg (57 eq.) of 5a dissolved in 113 μL of TEAB and incubated for 1 h. Water (0.7 mL) was added to hydrolyze the unreacted active ester. Both samples of protein hydrolysates, derivatized and non-derivatized, were evaporated on a speedvac. Subsequently, they were diluted 50 times with water and analyzed by LC-MS. The LC-MS analysis was performed on micrOTOF-Q coupled with the analytic HPLC Agilent 1200, equipped with the UV detector—210 and 280 nm, RP column: Aeris Peptide, Phenomenex XB-C18 (50 × 2.1 mm, 100 Å, 3.6 μm), flow—0.2 mL/min, injection volume—5 μL, eluents: A = H2O + 0.1% HCOOH, B = 80% MeCN in H2O + 0.1% HCOOH with the gradient: 0–5% B in 3 min, 5–60% B in 55 min., 60–100% B in 40 min. The separation was performed at room temperature (22 °C).
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3

Triterpenoid Extraction and Detection

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The extraction and detection of erythrydiol (2) follow the procedure described for β-amyrin. For the rest of the triterpenoids, 200 µl of culture was collected in a microfuge tube before it was directly extracted with 800 µl methanol with bead-beating (3,800 rpm, 1 min × 2). The mixture was centrifuged at 12,000g for 1 min to separate the pellet. Two hundred microlitres of the supernatant was transferred into an Eppendorf tube, which was then evaporated in a vacuum concentrator at room temperature and the remainders were resuspended in 200 µl methanol. Finally, samples were filtered with Amicon Ultra 0.5-ml 3-kDa filter tubes or centrifuged at 15,000g for 5 min. Products were analysed using LC–MS (1260 Infinity II LC-MSD iQ, Agilent) equipped with a reverse phase C18 column (Kinetex 2.6 µm, 250 × 4.6 mm, XB-C18, Phenomenex). A 50-min isocratic method was performed with 10:90 of water (solvent A) and acetonitrile (solvent B) using a flow rate of 0.3 ml min−1. Full mass spectra were generated for metabolite identification by scanning within the m/z range of 300–600 in negative-ion mode. Data acquisition and analysis were performed using OpenLab CDS version 2.4 (Agilent).
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4

Oleanolic Acid Pharmacokinetic Profiling

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OA was separated using a Phenomenex XB-C18 (50 × 2.1 mm, 2.6 µm) column. The mobile phase consisted of menthol and water with 10 Mm ammonium acetate (85:15, v/v). The flow rate was 0.2 ml/min at the first two minutes, and changed to 0.25 ml/min within 0.01 min. After maintaining there from 2.01 to 3.99 min, the flow rate returned to 0.2 ml/min in 0.01 min. The column temperature was maintained at 30 °C.
Detection of OA was performed in negative ion mode with an ESI source. Selective ion reaction (SIR) was applied to monitor the transitions of m/z 455.5 and m/z 469.5 for OA and IS, respectively, with a scan time of 0.2 sec. The capillary voltage was set at 2.54 kV. The cone voltage was 55 and 35 V for OA and IS, respectively. The ion source temperature and desolvation temperature was set at 120 and 500 °C. The method showed good linearity over the concentration range of 10–1000 ng/ml for OA. The pharmacokinetic parameters were calculated using DAS 2.1.1 software and the values were expressed as mean ± S.D.
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5

LC-MS Analysis of Vernonia Extracts

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For the LC-MS analyses, extracts of VpLAE and n-BF were prepared using 10 mg of the dry powder of each extract or fraction and 1 mL of a MeOH:H2O (7:3, v:v) solution with hydrocortisone (10 mg/mL) as an internal standard. Extraction was performed in an ultrasonic bath for 10 min at room temperature. The extracts were filtered through a 0.20 mm PTFE membrane before analysis. Chemical profiles were obtained on an Accela UHPLC instrument (Thermo Scientific™, Waltham, MA, USA) with a diode array ultraviolet light detector (UV-DAD) coupled to an ExactiveTM Plus mass spectrometer (Thermo Scientific™, Waltham, MA, USA) with electrospray ionization source and orbitrap analyzer. Chromatograms were acquired in positive and negative ionization modes using a C18 Kinetex column (1.7 µm, XB-C18, 150 mm × 2.1 mm, Phenomenex) and an elution gradient of water and acetonitrile both with 0.1% of formic acid. All other chromatographic and spectroscopic parameters followed the methodology employed by Gallon et al. (2018b). Metabolites detected in VpLAE and n-BF were putatively identified by comparing the spectroscopic data of each chromatographic signal with the data available in the in-house database of secondary metabolites reported for Vernonieae species.
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6

UHPLC-MS Analysis of Organic Compounds

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The analytical column was a Phenomenex Kinetex XB-C18 (150 mm × 2.1 mm, 2.6 μm) reversed-phase column. The mobile phases used for the separation consisted of distilled water with 0.1% formic acid (A) and methanol with 0.1% formic acid (B). The samples were analyzed in gradient mode as follows (A/B; v/v): 90:10 at 0 min, 80:20 at 0.74 min, 40:60 at 5.88 min, 10:90 at 10 min, 0:100 between 12 and 16 min, and 90:10 from 16.01 to 20 min. All samples were injected with a volume of 3 μL, and the mobile phase flow rate was kept at 0.2 mL/min. The column was kept at 40°C during the runtime. The UHPLC/MS system was composed of a Shimadzu Nexera UHPLC (pump, automatic sampler, and PDA analyzer, Shimadzu Corp, Kyoto, Japan) coupled with a Shimadzu LCMS2020 single quadrupole mass detector (Shimadzu Corp., Kyoto, Japan). MS was used with an ESI interface operating in positive ion mode.
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7

Quantitative Analysis of Marine Toxins

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Perform toxin analysis according to the method described by Nishimura et al. (44 (link)). A crude toxin extract (1 mL) was taken and mixed with 60 µL of 2.5 M NaOH, followed by incubation in a water bath at 70°C for 40 min. After cooling to room temperature, 60 µL of 2.5 M HCl was added to the mixture, which was then filtered through a 0.22-µm spin filter (Pall Corporation, USA) and stored at −20°C for subsequent analysis by liquid chromatography. The reference standards for the three DSTs (OA, DTX1, and DTX2) were procured from the National Research Council of Canada’s Institute for Marine Biosciences, and absolute quantification was performed. Regression curves were constructed based on the known toxin concentrations and spectral areas, enabling the quantification of toxin levels in the samples. Analytical software was utilized to visualize the toxin spectra and facilitate quantification. The determination and quantification of LC/MS were carried out using an HPLC system (Shimadzu Prominence LC-20ADXR) coupled with a tandem mass spectrometer (4500 QTRAP LC-MS/MS system, AB Sciex Instruments, Foster City, CA). Phenomenex Kinetex XB-C18 (150 × 2.1 mm, 2.6 µm) column was utilized for toxin separation, with the mobile phase consisting of acetonitrile (solvent A) and 0.15% formic acid in water (solvent B).
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8

Stability of Therapeutic Peptides: HPLC Analysis

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Peptides Ac-FAEDA, Ac-FAEPA, Ac-FAEAA, Ac-FAQDA, Ac-FAQPA and Ac-FAQAA (1 mg/mL) were incubated at either 37 °C or 60 °C in 50mM MOPS buffer at pH 6.7, 7.0 and 7.4 or 50mM sodium acetate buffer at pH 4.0. Aliquots were collected at various time intervals and were injected onto an Agilent 1100 HPLC using an Aeris RP-HPLC column (2.6 μ, XB-C18, 100 × 2.1 mm, Phenomenex). Breakdown products of peptides Ac-FAQDA and Ac-FAEDA were eluted with the following gradient 2% ACN, 0.1% TFA 0–40 min, 5% ACN, 0.1% TFA 40–60 mins, 10% ACN, 0.1%TFA 60–80 min, 15% ACN, 0.1% TFA 80–100min, 25% ACN, 0.1% TFA 100–120 min, 80 % ACN, 0.1%TFA, 135 min 2% ACN, 0.1%TFA 145min. All other peptides used the following elution gradient: 2% ACN, 0.1% TFA 5 min, 20% ACN, 0.1% TFA 15 mins, 40% ACN, 0.1%TFA 20 min, 25 min 80%ACN, 0.1% TFA, 35 min 80% ACN, 0.1% TFA, 30.1 min 2% ACN, 0.1%TFA, 40 min 2% ACN, 0.1%TFA.
Breakdown of all peptides was monitored at 216nm and 280nm. Peaks were collected and identified by tandem mass spectrometry on an LTQ Orbitrap Fusion Tribrid with a nanoelectrospray ionisation source (Thermo Scientific, San Jose, CA). Data were manually acquired with HCD collision energy set to 15.
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9

HPLC-MS/MS Analysis of Deoxyribonucleotides

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The deoxyribonucleotides produced from DNA hydrolysis were analyzed on a Shimadzu Nexera HPLC system (Columbia, MD, USA) coupled to a Sciex API 6500 triple quadrupole mass spectrometer with an IonDrive Turbo V source (Sciex, Foster City, CA, USA) in positive ion mode. The conditions were as follows: column, Phenomenex XB-C18 (100 mm × 2.1 mm, 2.6 μm); mobile phase A, water with 0.1% formic acid; mobile phase B, acetonitrile with 0.1% formic acid; gradient, 0–1.0 min, 0% B, 1.0–2.0 min, 0%–5% B, 2.0–2.5 min, 5%–95% B, 2.5–3.0 min, 95% B, 3.0–3.5 min, 95%–0% B, 3.5–4.0 min, 0% B; flow rate, 1.0 mL/min; column temperature, 50 °C; and injection volume, 10 μL.
The deoxyribonucleotides were quantitated in the multiple reaction monitoring (MRM) scan in the positive mode. The compound-dependent parameters are listed in Table 1, and the main instrument-dependent parameters were set as follows: ionspray voltage, 5500 V; ion source temperature, 500 °C; collision gas (CAD), -3; curtain gas (CUR), 30; nebulizer gas (GS1), 60; and turbo gas (GS2), 60.

Compound-dependent parameters in MS/MS analysis of mono-deoxyribonucleotides.

Table 1
AnalyteQ1(m/z)Q3(m/z)Dwell times (ms)DP(V)EP(V)CE(V)CXP(V)
dAMP3321365041102110
dTMP323207502610914
dCMP308112503110158
dGMP3481525031101712
IMP3491375041101712
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10

Investigating Gsu Intermediate Formation

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Attempts to promote the formation of a Gsu intermediate were undertaken using a Glu containing peptide Ac-YAETT. The peptide (2 mg) was initially dissolved in 50uL of 100% MeOH and acidified with a drop of concentrated HCl and incubated at RT for 30 min. Samples were dried down under vacuum and reconstituted in 0.1% TFA. Peptide containing Ac-YA(Glu-OCH3)TT were isolated by HPLC using an Aeris peptide RP-HPLC column (2.6 μ, XB-C18, 100 × 2.1 mm, Phenomenex) using the same gradient as shown above. All peptides containing methylated Glu residues were confirmed by tandem mass spectrometry and dried down before further experiments.
Ac-YA(Glu-OCH3)TT was incubated in 50mM MOPS 6.7 for 72 hrs at 60 °C. Formation of Gsu was monitored by HPLC using the method highlighted above. As the Gsu was unstable and could be only isolated in tiny quantities, the interaction of Ac-YA(Glu- OCH3)TT with free amino groups was examined. Ac-YA(Glu-OCH3)TT was incubated with a five molar excess of PE in 50 mM MOPS pH 6.7 at 60 °C. Aliquots were removed at selected times and analysed by RP-HPLC. Peaks corresponding to the peptides cross-linked with PE were identified by mass spectrometry.
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