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Lcq fleet ion trap mass spectrometer

Manufactured by Thermo Fisher Scientific
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The LCQ Fleet Ion Trap mass spectrometer is a laboratory instrument used for the analysis and identification of chemical compounds. It utilizes ion trap technology to capture, isolate, and detect ions based on their mass-to-charge ratio. The core function of the LCQ Fleet is to provide high-sensitivity analysis of complex mixtures, enabling the identification and characterization of various analytes.

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58 protocols using lcq fleet ion trap mass spectrometer

1

LC-MS Analysis of CoA Adducts

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Identification of β-valinyl-CoA and methyl-crotonyl-CoA was performed in a LCQ Fleet Ion Trap mass spectrometer (Thermo Scientific). Reaction components were separated by HPLC using an Alltech Altima HP C18 column (3 μm, 100 × 2.1 mm). The CoA adducts were eluted using eluent A (water, 0.1 % formic acid) with an elution gradient of eluent B (acetonitrile, 0.08 % formic acid; 0–2 min, 0–2 %; 2–20 min, 2–15 %; 20–32 min, 15–80 %; 32–37 min, 80 %; 37–38 min, 80 0 %; 38–48 min, 0 % eluent B). The samples were analyzed in a negative ion mode, and mass spectra were collected over a scan range of m/z 500–1000. Typical retention times were 13 min for β-valinyl-CoA (m/z 864; M–H) and 28 min for methyl-crotonyl-CoA (m/z 847; M–H).
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2

Analytical Techniques for Natural Product Isolation

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Thin-layer chromatography was carried out using pre-coated silica Q-gel 60 F254 plates (0.25 mm, Merck). Column chromatography (CC) was conducted using silica gel (Kieselgel 60, 230–400 mesh, Merck), and Sephadex LH-20 (18–111 µm, GE Healthcare AB, Stockholm, Sweden). HPLC was performed using the Varian Prostar 210 system. A YMC-Pack ODS-A column (5 μm, 250 × 20 mm i.d., YMC, Kyoto, Japan) was used for preparative HPLC analysis with an 8 mL/min flow rate. ESI-MS was performed on an LCQ Fleet Ion Trap mass spectrometer (Thermo Scientific, Madison, WI, USA). NMR spectral data were acquired by using a Varian 500-MHz NMR spectrometer (Inova 500 Spectrometer, Varian, Palo Alto, CA, USA). Tetramethylsilane was used as an internal standard, and chemical shifts data were expressed as δ value.
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3

Optimized Synthesis of Compound 6e

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All commercial materials and solvents (> 95% purity grade) were purchased from Merck KGaA (Darmstadt, Germany) and used without further purification. All reactions were carried out under a nitrogen atmosphere, unless otherwise noted. All reactions were monitored by thin layer chromatography (TLC) on precoated silica gel 60 F254; spots were visualized with UV light, or by treatment with a 1% aqueous KMnO4 solution, or with a hydroalcoholic curcumin solution (100 mg of curcumin in a 100 mL solution of ethanol with 2 N HCl (99:1 v/v)). Products were purified by flash chromatography (FC) on silica gel 60 (230–400 mesh). Yields refer to isolated compounds estimated to be >95% pure as determined by 1H-NMR. NMR spectra were recorded on 300 or 400 MHz Bruker spectrometers, using tetramethylsilane (TMS) as the internal standard. Supplementary materials for 13C-NMR, the APT pulse sequence was adopted. Chemical shifts are reported in parts per million relative to the residual solvent. Multiplicities in 1H-NMR are reported as follows: s = singlet, d = doublet, t = triplet, m = multiplet, br s = broad singlet. High-resolution MS spectra (HR-MS) were recorded with a Thermo Fisher LCQ Fleet ion trap mass spectrometer, equipped with an ESI source. The purity of compound 6e was confirmed to be >95% by means of elemental analysis on a CHN PerkinElmer 2400 instrument.
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4

Mycotoxin Analysis via LC-MS/MS

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Culture extracts were screened for the presence of ENNs, BEA, BEAE and ALLOBEA analogues using an LCQ Fleet ion trap mass spectrometer (Thermo Fisher Scientific) coupled to a Waters Acquity UPLC (Milford, MA, USA) with chromatographic column—SunFire C18; instrumental conditions were described earlier by Urbaniak et al. 2019 [3 (link)].
Quantitative analysis of mycotoxins (BEA and ENNs) were performed using an LC-MS/MS instrument consisting of an UPLC™ system (Acquity, Waters, Milford, MA, USA) coupled to a triple quadrupole mass spectrometer (TQD, Waters Micromass, Manchester, UK), equipped with an electrospray ionization interface according to Stanciu et al. [67 (link)] with our own modifications, described below. The separation of beauvericin and enniatins was achieved using a BEH C18 chromatographic column (100 × 2.1 mm i.d., 1.7 µm particle size; Waters) with injection volume—3 µL and flow rate of mobile phase—0.3 mL/min. The mobile phase consisted of water (A) and methanol (B), both containing 5 mM ammonium formate and 0.1% (v/v) formic acid. The gradient program was as follows: initial conditions at 80% A, 20% B for 2 min; then, from 20% to 90% B in 5 min; next, 90% B for 6 min; from 90% to 100% B in 3 min; return to initial conditions in 2 min. For data processing, EmpowerTM 1 software was used (Waters, Manchester, UK). Chromatographic parameters are shown in Table 5.
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5

Comprehensive LC-MS/MS Analysis of Metabolites

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The analyses were performed using a Thermo Scientific LCQ FLEET system consisting of an LCQ FLEET ion trap mass spectrometer, a Surveyor MS Pump/Autosampler/PDA Detector (Thermo Fisher Scientific, Waltham, MA, USA) through an ESI source. The separation was obtained by using a Gemini® C18 110 A analytical column (150 × 2.00 mm i.d., 5 μm) and the pre-column (Phenomenex, Torrance, CA, USA). The mobile phase consisted of aqueous formic acid at 0.1% and acetonitrile (solvent B) at 0.3 mL/min (the injection volume was 10 µL). A linear solvent gradient was used as follows: from 10% B to 95% B in 25 min with a final plateau of 3 min at 100% B. The ion trap operated in data-dependent, full scan (60–2000 m/z), and MSn mode to obtain fragment ions m/z with a collision energy of 35% and an isolation width of 3 m/z. The negative and positive parameters of the ion mode ESI source have been optimized to an ionization voltage of 5.0 kV, a capillary temperature of 320 °C, a capillary voltage of 32 V, a sheath gas flow rate of 25 arbitrary units (AU), and an auxiliary gas flow rate of 10 AU. Data was acquired using Thermo Excalibur 2.2 software (Thermo Fisher Scientific, MA, USA).
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6

Rapid UHPLC-MS/MS Quantification

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Chromatographic partition was achieved by using a Thermo Scientific, Aquasil C18 column (100×2.1 mm, 5 µm particle size) attached to Thermo Dionex Ultimate 3000 UHPLC with a quaternary pump, autosampler, solvent manager, and an MS-MS detector (Thermo Scientific LCQ Fleet, Ion Trap mass spectrometer, Serial# LCF 10356, San Jose, CA, USA). Ammonium acetate buffer (1 mM, pH 4.4) and methanol (20:80, v/v) were used as the mobile phase in nongradient elution mode at a flow rate of 300 µL/min. The injected sample volume was 10 µL. The column temperature was maintained at 40°C±2°C, and temperature of autosampler was maintained at 4°C±2°C. The chromatographic run time was 3 minutes.
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7

Quantifying Metabolites in B. coagulans Fermentation

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Analysis of lactic acid, sugars and other fermentation products of B. coagulans which may occur such as ethanol and acetic acid was performed using a Waters e2695 HPLC system (Milford USA) equipped with Waters RI2414 and Waters UV/Vis 2489 (measuring at 210 nm) detectors. The column used was a Shodex RS pak KC-811 ion exchange column (length 300 mm, I.D. 8 mm), controlled at 65 °C. As eluent, 3 mM H2SO4 in milli-Q water was used. The flow used was 1 mL/min. Samples obtained during fermentation were de-frozen prior to analysis. Two hundred fifty microlitres of this sample was mixed with 250 μL of internal standard, containing 0.25 g/L phthalic acid and 500 μL of milli-Q water. Samples were filtered using 0.2 μm Spartan filters, and supernatants were measured using HPLC.
To determine furan concentrations, UPLC-MS/MS measurements were performed using a Dionex Ultimate 3000 RSLC system, equipped with a Waters Acquity BEH C18 RP column, in combination with a Thermo ScientificTM LCQ Fleet Ion Trap Mass Spectrometer, as previously described (van der Pol et al. 2015 (link)).
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8

Purification and Characterization of Peptides from Hylarana guentheri Skin Secretion

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Five mg of lyophilized skin secretion of Hylarana guentheri was dissolved in 0.5 mL of trifluoroacetic acid (TFA)/water and centrifuged at 2500× g for 5 min. Then the supernatant was pumped to reverse-phase HPLC with the analytical Jupiter C-5 column (250 × 4.6 mm, Phenomenex, UK) and eluted with a 0–100% linear gradient program from water/TFA (99.95/0.05, v/v) to acetonitrile/water/TFA (80/19.95/0.05, v/v/v). The whole program ran over 240 min at a flow rate of 1 mL/min. Fractions were collected at 1 min intervals, and all samples were subjected to time-of-flight mass spectrometry (MALDI-TOF MS) (Voyager DE, Perspective Biosystems, Foster City, CA, USA). The instrument was calibrated in the range of 1–4 kDa, and the accuracy of mass determinations was ±0.1%. The fraction which contained peptides with same molecular mass as that predicted from cloned cDNA, was injected to analyses the primary structure by LCQ-Fleet ion-trap mass spectrometer (Thermo Fisher Scientific, San Francisco, CA, USA).
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9

Analytical Characterization of Compounds by LCMS and NMR

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Samples were analyzed by LCMS on an UltiMate 3,000 LC System coupled to a LCQ Fleet Ion Trap Mass Spectrometer (Thermo Scientific). Chromatographic separation was performed on a Hypersil Gold aQ C18 column (150 × 2.1 mm, 3 µm particle size). Water (A) and acetonitrile (B) were used as the eluents, both supplemented with 0.1% formic acid. The separation method was performed at 0.7 ml/min using a gradient as follows: 5% B at 0 min to 95% B by 8 min followed by washing the column at 100% B for 2 min and re‐equilibration of the column at 5% B for 2 min prior to the next injection. HR‐ESI‐MS spectra were recorded with a Thermo LTQ‐FT Ultra coupled with a Dionex UltiMate 3,000 HPLC system.
NMR spectra were recorded on Bruker AVHD300, Bruker AVHD400, Bruker AVHD500 (only 1H NMR spectra), or Bruker AV500‐cryo spectrometers. The chemical shifts are listed as parts per million (ppm) and refer to (TMS; Tetramethylsilane) = 0. The spectra were calibrated using residual undeuterated solvent as an internal reference (CDCl3 = 7.26 ppm, (CD3)2CO = 2.05 ppm, (CD3)2SO = 2.50 ppm, CD3OD = 3.31 for 1H NMR; CDCl3 = 77.0 ppm, (CD3)2CO = 29.8 ppm, (CD3)2SO = 39.5 ppm, CD3OD = 49.0 for 13C NMR).
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10

Peptide Analysis by ESI-MS

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Electrospray
ionization mass spectrometry was performed on an LCQ Fleet Ion Trap
mass spectrometer (Thermo Scientific). Peptide masses were calculated
from the experimental mass to charge (m/z) ratios from the observed multiply charged species of a peptide.
Deconvolution of the experimental MS data was performed with the software
package MagTran v1.03.
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