Sciex 4000 qtrap mass spectrometer

Manufactured by AB Sciex

Sourced in United States

The SCIEX 4000 QTRAP mass spectrometer is a high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) system. It features a triple quadrupole design with a linear ion trap for enhanced sensitivity and selectivity in quantitative and qualitative analyses. The system is capable of performing a variety of MS/MS experiments, including precursor ion scan, product ion scan, and multiple reaction monitoring (MRM) for targeted compound analysis.

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Lab products found in correlation

Colorimetric assay kit, by Cayman Chemical (1 mentions) Multiquant software, by Thermo Fisher Scientific (1 mentions) Acquity uplc beh c18 analytical column, by Waters Corporation (1 mentions) Acquity uplc system, by Waters Corporation (1 mentions) Analyst software 1, by AB Sciex (1 mentions) Agilent 1200, by Agilent Technologies (1 mentions) Dd2 spectrometer, by Agilent Technologies (1 mentions) P 2000 digital polarimeter, by Jasco (1 mentions) 515 hplc pump, by Waters Corporation (1 mentions) Apex ft icr mass spectrometer, by Bruker (1 mentions) Evolution 201 spectrophotometer, by Thermo Fisher Scientific (1 mentions) Ultraflextreme maldi tof tof mass spectrometer, by Bruker (1 mentions)

11 protocols using sciex 4000 qtrap mass spectrometer

Lipidomics of ASC Adipocytes

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Total TG levels were measured using a colorimetric assay kit (Cayman Chemicals). Protein concentration was used to normalize intracellular TG content. For lipidomics, after 5 days of transgene expression ASC adipocytes were washed with fresh medium. Ice-cold isopropanol was added, and cells were scraped and collected into cold tubes. Extracts were incubated for 1 hr at 4°C, than vortexed and centrifuged at 2,300 × g for 10 min. The supernatant was used for mass spectroscopic analysis. All data were acquired using a Sciex 4000 QTRAP mass spectrometer as previously described (Rhee et al., 2011 (link)). MultiQuant software (version 1.1; Applied Biosystems/Sciex) was used for automated peak integration, and peaks were manually reviewed for quality of integration. Internal standard peak areas were monitored for quality control and used to normalize analyte peak areas.
For the transduced ASCs we averaged six replicates for metabolite abundance of 44 TG species and computed an abundance ratio of the two (IRF1/rtTA). We built a regression model, predicting the abundance ratio using number of double bonds and total number of carbon atoms as variables as well as an interaction term to assess whether the relationship with number of double bonds varies with carbon number. Statistical significance of regression coefficients was assessed using the F test.

Friesen M., Camahort R., Lee Y.K., Xia F., Gerszten R.E., Rhee E.P., Deo R.C, & Cowan C.A. (2017). Activation of IRF1 in Human Adipocytes Leads to Phenotypes Associated with Metabolic Disease. Stem Cell Reports, 8(5), 1164-1173.

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CRV431 Quantification by LC-MS/MS

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Samples were analyzed by LC-MS/MS on a SCIEX 4000 QTrap mass spectrometer (Sciex, Rewood City, CA, USA). CRV431 samples were injected onto an Acquity UPLC BEH C18 analytical column (50 × 2.1 mm, 1.7 μm, Waters, Milford, MA, USA) and separated using a methanol-water gradient system (Table 1). The ammonium adducts of CRV431 (mass transition 1321.5/1304.5) were analyzed by mass spectrometry using electrospray ionization (ESI) in positive ion mode. The electrospray voltage was set at 4500 volts.

Trepanier D.J., Ure D.R, & Foster R.T. (2017). In Vitro Phase I Metabolism of CRV431, a Novel Oral Drug Candidate for Chronic Hepatitis B. Pharmaceutics, 9(4), 51.

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Liver Metabolite Profiling by UHPLC-MS/MS

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Liver specimen metabolites and standard analyte solutions were separated by liquid phase chromatography using a Nexera X2 Ultra-High-Performance Liquid Chromatography (UHPLC) system (Shimadzu, Kyoto, Japan) at 40 °C with 3 µL injections on a Poroshell 120 EC-C18 2.1 mm × 75 mm × 2.7 µm UHPLC column (Agilent Technologies, Santa Clara, CA, USA) following a Poroshell 120 EC-C18 2.1 mm × 5 mm × 2.7 µm UHPLC guard column (Agilent Technologies, USA). To perform this, gradient elution with an initial mobile phase was used, consisting of 95%: 10 mM tributylamine and 15 mM acetic acid in water, pH 5.2; 5%: acetonitrile:water (95:5, v/v) fortified with 0.1% formic acid; this was performed at a flow rate of 0.75 mL/min. Standard and sample metabolites were detected using negative electrospray ionization on a SCIEX 4000 Qtrap mass spectrometer (Framingham, MA, USA). MS/MS parameters were optimized for each metabolite and quantified using SCIEX MultiQuant 3.0.2 (Framingham, USA) according to calibration curves (0.15 to 12,000 pmol per injection) of pure analytes purchased from Sigma Aldrich (Oakville, ON, Canada), prepared in water. Values were normalized per mg of tissue.

Tambay V., Raymond V.A., Goossens C., Rousseau L., Turcotte S, & Bilodeau M. (2023). Metabolomics-Guided Identification of a Distinctive Hepatocellular Carcinoma Signature. Cancers, 15(12), 3232.

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Serum PFAS Measurement Protocol

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Measurement of PFASs in collected sera was conducted using the method as detailed previously [59 (link)]. Briefly, 100 μL of serum was diluted in formic acid and spiked with isotopically labeled internal standards before injection into the automated on-line solid phase extraction method coupled to liquid chromatography and tandem mass spectrometry (Symbiosis ™ Pharma, IChrom Solutions, Plainsboro, NJ, and Sciex 4000 QTrap mass spectrometer, Sciex, Redwood City, CA) for clean-up and analysis. Native and isotopically-labeled PFAS standards were purchased from Wellington Laboratories (Shawnee Mission, KS). Within each batch analysis of 20 actual samples, two in-house spiked calf serum samples and NIST 1958 Standard Reference Material were run in duplicate for quality control. The laboratory is proficient in serum PFAS analysis as demonstrated by successful regular participation in proficiency testing (CDC, AMAP).

Hurley S., Goldberg D., Wang M., Park J.S., Petreas M., Bernstein L., Anton-Culver H., Nelson D.O, & Reynolds P. (2018). Breast cancer risk and serum levels of per- and poly-fluoroalkyl substances: a case-control study nested in the California Teachers Study. Environmental Health, 17, 83.

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Lipid Profiling of Acellular Conditioned Media

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Lipids were isolated from three-day ACM by lipid extraction as described previously (Verheijen et al., 2009) . Neutral lipids were analyzed by reverse phase HPLC-tandem mass spectroscopy on a Sciex 4000 Q-trap mass spectrometer (Sciex, Framingham, MA), equipped with an atmospheric pressure chemical ionization source. Intact phospholipids were analyzed by HILIC chromatography and mass spectrometry as described previously (Arroyo-Olarte et al., 2015) . Levels of detected lipids in ACM were normalized to total protein content.

van Deijk A.F., Camargo N., Timmerman J., Heistek T., Brouwers J.F., Mogavero F., Mansvelder H.D., Smit A.B, & Verheijen M.H. (2017). Astrocyte lipid metabolism is critical for synapse development and function in vivo. Glia, 65(4).

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Quantifying Intracellular Cyanotoxins: LC-MS/MS Analysis

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Intracellular cyanotoxins were extracted from filters applying the protocol described by Cerasino and Salmaso [48 (link)] and quantified with LC-MS/MS. The extraction was carried out by using a mixture of acetonitrile in water (60/40 v/v), containing 0.1% formic acid. Extracted toxins were injected into a LC-MS/MS system, composed of a Waters Acquity UPLC system (Waters, Milford, MA, USA) coupled to a SCIEX 4000 QTRAP mass spectrometer (AB Sciex Pte. Ltd., Singapore). The mass detector was operated in scheduled MRM (Multiple Reaction Monitor) mode, using positive electrospray ionisation (ESI+). Quantification of microcystins was performed following the protocol from Cerasino and Salmaso [48 (link)], which has the capability of determining the 11 most common microcystin variants, namely RR, [D-Asp3]-RR (RRdm), [D-Asp3]-HtyrR (HtyRdm), YR, LR, [D-Asp3]-LR (LRdm), WR, LA, LY, LW, LF. Analysis of cylindrospermopsins and saxitoxins was performed following the protocol from Ballot et al. [49 (link)], targeting CYN, STX, dcSTX, NeoSTX, GTX1, GTX4, GTX5, C1 and C2.

Zupančič M., Kogovšek P., Šter T., Remec Rekar Š., Cerasino L., Baebler Š., Krivograd Klemenčič A, & Eleršek T. (2021). Potentially Toxic Planktic and Benthic Cyanobacteria in Slovenian Freshwater Bodies: Detection by Quantitative PCR. Toxins, 13(2), 133.

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Quantitative LC-MS/MS Analysis of GdPC

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To identify GdPC, an LC-MS/MS method for the physiological metabolite CDP choline (C0256, Sigma Aldrich Co Ltd., Dorset, UK) based on the method by (Desoubzdanne et al, 2010 (link)) was developed. A Sciex 4000 Q trap mass spectrometer (AB Sciex UK Ltd., Warrington, UK) fitted with a Turbo ionspray source at 500 °C operated in positive mode was used. Quantitative data acquisition was done using the software Analyst ver 1.4.2 (Ab Sciex UK Ltd.). Given the similarities in structure between CDP choline and GdPC (Figure 2A and B), their chromatographic properties were also expected to be similar. PDAC tissue, obtained from a mouse 2 h after IP injection of dFdC (100 mg kg⁻¹), was precipitated using 100% acetonitrile. After centrifugation, the supernatant was transferred to a clean tube and evaporated to dryness. The residue was reconstituted in 75% acetonitrile and injected into the mass spectrometer. An enhanced product ion scan for the expected precursor ion for GdPC (m/z 509) was run (under the same conditions as for the multiple reaction monitoring experiment for CDP choline). The spectra obtained were compared with those of CDP choline to aid identification of GdPC.

Bapiro T.E., Frese K.K., Courtin A., Bramhall J.L., Madhu B., Cook N., Neesse A., Griffiths J.R., Tuveson D.A., Jodrell D.I, & Richards F.M. (2014). Gemcitabine diphosphate choline is a major metabolite linked to the Kennedy pathway in pancreatic cancer models in vivo. British Journal of Cancer, 111(2), 318-325.

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Quantitative Sphingolipid Analysis by LC-MS/MS

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The sphingolipids were analyzed using previously reported method^{25 (link)} with modification. Briefly, cell pellet (7.5 × 10⁶ cells) added with 50 µl of internal standard (C17:0-ceramide, 1 pM) was extracted twice with ethyl acetate/2-propanol/water (60/28/12; v/v/v). Sphingolipids were separated using gradient elution with mobile phase A (2 mM ammonium formate and 0.2% formic acid (v/v) in water) and B (1 mM ammonium formate and 0.2% formic acid (v/v) in methanol) on an Agilent 1200 series high-performance liquid chromatography (HPLC) system with Spectra C8SR column (3 µm, 150 × 3.0 mm, Peeke Scientific, Redwood, CA). Mass spectrometric detection was performed by multiple reaction monitoring (MRM) mode on a Sciex 4000 QTRAP mass spectrometer (AB Sciex, Framingham, MA) operating in positive ion mode. Analyst software 1.6.3 (AB Sciex) was used for the data acquisition as well as processing. Sphingolipid data generated from liquid chromatography-tandem mass spectrometry (LC-MS/MS) were normalized to lipid phosphate as previously described^{26 (link)}.

Verlekar D., Wei S.J., Cho H., Yang S, & Kang M.H. (2018). Ceramide synthase-6 confers resistance to chemotherapy by binding to CD95/Fas in T-cell acute lymphoblastic leukemia. Cell Death & Disease, 9(9), 925.

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Lipid and Fatty Acid Profiling of Myelin

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Myelin was purified by density gradient centrifugation [48 (link)], and lipids were isolated by lipid extraction, as described previously [6 (link)]. Analysis of neutral lipids was done using a Sciex 4000 Q-trap mass spectrometer (AB Sciex, Framingham, MA, USA), equipped with an atmospheric pressure chemical ionization source. Analysis of free fatty acids was done after mild alkaline hydrolysis of isolated phospholipid fractions from lipid extracts, as described previously[5 (link),6 (link)]. Analysis of intact phospholipids were analyzed using defined molecular species and authentic free fatty acid standards, as described previously[5 (link),6 (link)].

Camargo N., Goudriaan A., van Deijk A.L., Otte W.M., Brouwers J.F., Lodder H., Gutmann D.H., Nave K.A., Dijkhuizen R.M., Mansvelder H.D., Chrast R., Smit A.B, & Verheijen M.H. (2017). Oligodendroglial myelination requires astrocyte-derived lipids. PLoS Biology, 15(5), e1002605.

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Pharmacokinetics of Niclosamide and JMX0207 in Mice

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Two to three month-old female B6 mice were used for the study. Four to five mice per group were given niclosamide (40 mg/kg in 1% DMSO and 0.5% carboxymethylcellulose) or JMX0207 in the same vehicle at the indicated dose by oral gavage. Sample preparation and liquid chromatography with tandem mass spectrometry (LC-MS/MS) detection of niclosamide and JMX0207 were essentially the same as described in a previous study and were performed using a Sciex 4000 Q-Trap mass spectrometer (AB SCIEX, Framingham, MA) with the Agilent 1200 high-performance liquid chromatography system (Agilent Technologies, Santa Clara, CA).^{29 (link)} JMX0207 was monitored at m/z 336/171. Declustering potential, entrance potential, collision energy, and collision cell exit potential were optimized for detection and quantification of JMX0207 at −45, −10, −35, and −14 V, respectively. Data from 4 or 5 mice at each time point were averaged and used to calculate pharmacokinetic parameters, using a pharmacokinetic solver (Microsoft, Redmond, WA) by assuming a noncompartmental model. Statistical significance of various data comparisons was determined with the use of GraphPad Prism (GraphPad Software, La Jolla, CA). The Student’s t test was used. P values < 0.05 were considered statistically significant.

Li Z., Xu J., Lang Y., Fan X., Kuo L., D’Brant L., Hu S., Samrat S.K., Trudeau N., Tharappel A.M., Rugenstein N., Koetzner C.A., Zhang J., Chen H., Kramer L.D., Butler D., Zhang Q.Y., Zhou J, & Li H. (2020). JMX0207, a Niclosamide Derivative with Improved Pharmacokinetics, Suppresses Zika Virus Infection Both In Vitro and In Vivo. ACS infectious diseases, 6(10), 2616-2628.

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