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Qtrap5500 mass analyzer

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The QTRAP5500 mass analyzer is a hybrid triple quadrupole-linear ion trap mass spectrometer designed for high-performance quantitation and qualitative analysis. It features a quadrupole-based mass filter and a linear ion trap for enhanced sensitivity and selectivity.

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Lab products found in correlation

Strata x column, by Phenomenex (2 mentions) Multiquant software, by AB Sciex (2 mentions) Lipidview, by AB Sciex (1 mentions) Analyst 1, by AB Sciex (1 mentions) Multiquant, by AB Sciex (1 mentions) Luna c18 column, by Phenomenex (1 mentions)

8 protocols using qtrap5500 mass analyzer

1

Targeted Plasmalogens Analysis by LC-MS

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Tissues were homogenized using zirconium beads and a high-frequency oscillator (Precellys) in phosphate-buffered saline (PBS) pH 7.2 at a ratio of 9:1 (buffer to tissue by weight). Homogenate containing about 2 mg protein was supplemented with deuterated internal standards (100 ng each of pPC 18:0/18:1-d9 and pPE 18:0/18:1-d9) and total lipids were extracted using methyl tert-butyl ether.33 (link) The extracted lipids were analyzed by LC–MS for plasmalogens PC, and plasmalogens PE using targeted analysis as described earlier34 (link) using a QTRAP5500 mass analyzer (Sciex).
Taylor E.L, & Taylor T.N. (1992). Reproductive biology of the Permian Glossopteridales and their suggested relationship to flowering plants.. Proceedings of the National Academy of Sciences of the United States of America, 89(23), 11495-11497.
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2

Murine Bone Marrow Lipid Profiling

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Whole BM was flushed from mouse hind limbs (femurs and tibias) with ice cold PBS. Samples were flash frozen on dry ice before shipment to Wayne State University Lipidomics Core facility for analysis. Fatty acyl lipidomic analysis was performed as per published procedures.31 (link), 32 (link) Briefly, the frozen samples were thawed on ice at the time of analysis, and homogenized using Zirconium beads (Precellys, Biotage). The homogenate was extracted for fatty acyl lipids using StrataX columns (Phenomenex) following supplementation with internal standards. The extracts were analyzed by LC-MS/MS using Multiple Reaction Monitoring (MRM) method on a QTRAP5500 mass analyzer (Sciex). Identities of the individual lipid mediators were confirmed from the retention times and spectra recorded for each detected peak and were quantified relative to the internal standards. The data were normalized against protein content of the samples (ng/mg protein).
Grazda R., Seyfried A.N., Maddipatti K.R., Fredman G, & MacNamara K.C. (2023). Resolvin E1 improves efferocytosis and rescues severe aplastic anemia in mice. bioRxiv.
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3

Lipidomic Analysis of Murine Skin

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Skin surface of euthanized mice were scraped with scalpels to obtain samples for LC-MS analysis. The samples were analyzed by LC-MS using standardized methods at the Lipidomics Core Facility at Wayne State University on a QTRAP5500 mass analyzer (Sciex) and the data were analyzed using LipidView (Sciex, version 1.2). The free fatty acids and triglycerides were quantitated against the spike internal standards.
Kobayashi T., Voisin B., Kim D.Y., Kennedy E.A., Jo J.H., Shih H.Y., Truong A., Doebel T., Sakamoto K., Cui C.Y., Schlessinger D., Moro K., Nakae S., Horiuchi K., Zhu J., Leonard W.J., Kong H.H, & Nagao K. (2019). Homeostatic Control of Sebaceous Glands by Innate Lymphoid Cells Regulates Commensal Bacteria Equilibrium. Cell, 176(5), 982-997.e16.
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4

Targeted Lipidomic Analysis of Oxidized LA Metabolites

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Targeted lipidomic analysis to measure plasma levels of bioactive oxidized metabolites of LA was performed by the Wayne State University Lipidomic Core Facility, as described.(35, 36) Briefly, samples in 150 µL methanol were spiked with 5 ng each of 15(S)‐HETE‐d8 and 14(15)‐ epoxyeicosatrienoic acid‐d8 as internal standards for recovery and quantitation and mixed thoroughly. The samples were then extracted for PUFA metabolites using C18 extraction columns. The extracted samples were analyzed for metabolites of LA (hydroxy, epoxy, keto, and dihydroxy metabolites) by liquid chromatography–mass spectrometry using the QTRAP5500 mass analyzer (Sciex).
Warner D., Vatsalya V., Zirnheld K.H., Warner J.B., Hardesty J.E., Umhau J.C., McClain C.J., Maddipati K, & Kirpich I.A. (2021). Linoleic Acid‐Derived Oxylipins Differentiate Early Stage Alcoholic Hepatitis From Mild Alcohol‐Associated Liver Injury. Hepatology Communications, 5(6), 947-960.
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5

Lipidomic Analysis of Whole Bone Marrow

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Whole BM was flushed from femurs and tibias, flash-frozen on dry ice, and shipped to Wayne State University Lipidomics Core facility for analysis. Fatty acyl lipidomic analysis was performed as per published procedures [30 (link), 31 (link)]. Samples were homogenized using Zirconium beads (Precellys, Biotage) and the homogenate was extracted for fatty acyl lipids using StrataX columns (Phenomenex) following supplementation with internal standards. Extracts were analyzed by LC–MS/MS using Multiple Reaction Monitoring method on a QTRAP5500 mass analyzer (Sciex). Identities of individual lipid mediators were confirmed from retention times and spectra recorded for each detected peak and were quantified relative to internal standards. Data were normalized against protein content of the samples (ng/mg protein).
Grazda R., Seyfried A.N., Maddipati K.R., Fredman G, & MacNamara K.C. (2024). Resolvin E1 improves efferocytosis and rescues severe aplastic anemia in mice. Cell Death & Disease, 15(5), 324.
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6

MRM Analysis of Acyl-CoA Metabolites

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Liver sample preparation and MRM of parent-daughter ion combinations for short and long-chain acyl Coenzymes A were conducted following the standard protocol detailed earlier [32 (link),33 ]. Chromatographic conditions are as follows: The samples are injected on reverse phase HPLC column (Phenomenex, Hydro RP, 3 μ, 2.1 × 150 mm) and eluted with gradient between water and acetonitrile containing 0.1 % ammonium acetate by weight. The gradient for acetonitrile is 0 min – 0 %, 5 min – 65 %, at a flow rate of 0.2 ml/min. The HPLC eluate is directly introduced to ESI source of QTRAP5500 mass analyzer (ABSCIEX) in the positive ion mode with the following conditions: Curtain gas: 35 psi, GS1: 45 psi, GS2: 45 psi, Temperature: 600 °C, Ion Spray Voltage: 5500 V, Collision gas: low, Declustering Potential: 60 V, Collisional energy: 53 eV, and Entrance Potential: 10 V. The data are collected using Analyst 1.6.2 software and the MRM transition chromatograms are quantitated by MultiQuant software (both from ABSCIEX). The internal standard (C-17 analogs of the sphingolipids) signal in each chromatogram is used for normalization for recovery as well as relative quantitation of each analyte.
Description of additional materials is presented in the Supplementary Data.
Brot N., Redfield B., Qiu N.H., Chen G.J., Vidal V., Carlino A, & Weissbach H. (1994). Similarity of nucleotide interactions of BiP and GTP-binding proteins.. Proceedings of the National Academy of Sciences of the United States of America, 91(25), 12120-12124.
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7

Fatty Acid Profiling in NAFLD and HCC

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Plasma collected at 32 and 55 weeks of age and tissue collected at 55 weeks of age were analyzed for fatty acid levels. Plasma samples were randomly selected from mice fed the CD -HFSC diet that had HCC (n = 5), mice with regenerative or dysplastic nodules without HCC (pre-malignant nodules; n = 5), and HCC-free mice fed the control diet with NAFLD (n = 5). Five tissue samples from HCCs obtained from the same mice were also analyzed.
Plasma (n = 30) and tissue (n = 5) samples were prepared for analysis through dilution and homogenization of tissue samples in a phosphate buffer using a bead homogenizer (Precellys, Bertin Technologies). Samples were adjusted to a final volume of 0.5-1 mL with LC-MS grade water, acidified with dilute hydrochloric acid and extracted with isooctane-ethyl acetate. Extracts were then dried and reconstituted in methanol-water-ammonium acetate. The extracts were sent to the Lipidomics Core Facility at Wayne State University for fatty acid metabolomics analysis. The extracts were subjected to HPLC on Targa C8 column and directly introduced to the QTRAP5500 mass analyzer (ABSCIEX). The data were collected using Analyst 1.6.2 software and the chromatograms were quantitated by MultiQuant software (ABSCIEX). In total 30 fatty acids (C12-C26) were analyzed (Supplemental Table S2).
Vlock E.M., Karanjit S., Talmon G, & Farazi P.A. (2020). Reduction of Polyunsaturated Fatty Acids with Tumor Progression in a Lean Non-Alcoholic Steatohepatitis-Associated Hepatocellular Carcinoma Mouse Model. Journal of Cancer, 11(19), 5536-5546.
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8

Eicosanoid Profiling from Mouse Plasma

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Mass spectrometry based eicosanomic analysis for eicosanoids derived from both arachidonic acid and eicosapentaenoic acid was performed on the plasma extracts collected from mice as described earlier (30 (link), 31 ). Briefly, plasma samples were spiked with a mixture of internal standards (5 ng each of PGE1-d4, LTB4-d4, and 15-HETE-d8), diluted with methanol to 15%, and applied to C18 solid phase extraction cartridges, washed sequentially with 15% methanol in water and hexane, followed by elution of the eicosanoids with methanol containing 1% formic acid. The eluates were evaporated to dryness and reconstituted in HPLC mobile phase for LC-MS analysis.
Eicosanomic analysis was performed by LC-MS using Luna C18 column (3µ, 2×150 mm, Phenomenex) for HPLC resolution of the eicosanoids and detected by QTRAP5500 mass analyzer (ABSCIEX) using optimized conditions for each eicosanoid by Multiple Reaction Monitoring (MRM) method as described before (31 ). LC-MS chromatograms were analyzed by MultiQuant (ABSCIEX) for quantitation of each eicosanoid and normalized to the internal standard signal. Under the standard conditions of the method, the detection limits for most of the eicosanoids were <2 pg on the column with a signal/ratio of 3.
Vasudevan A., Yu Y., Banerjee S., Woods J., Farhana L., Rajendra S.G., Patel A., Dyson G., Levi E., Maddipati K.R., Majumdar A.P, & Nangia-Makker P. (2014). Omega-3 fatty acid is a potential preventive agent for recurrent colon cancer. Cancer prevention research (Philadelphia, Pa.), 7(11), 1138-1148.
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