Lxq linear ion trap mass spectrometer

Manufactured by Thermo Fisher Scientific

Sourced in United States

The LXQ linear ion trap mass spectrometer is a versatile analytical instrument used for the identification and quantification of a wide range of chemical compounds. It utilizes a linear ion trap design to capture and analyze ions, providing high sensitivity and resolution for various applications.

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Lab products found in correlation

Bioworks, by Thermo Fisher Scientific (4 mentions) Accela lc system, by Thermo Fisher Scientific (4 mentions) Xcalibur software, by Thermo Fisher Scientific (1 mentions) 1260 infinity quaternary hplc system, by Agilent Technologies (1 mentions) Diode array detector, by Agilent Technologies (1 mentions) Agilent 1100 series hplc, by Agilent Technologies (1 mentions) Q tof mass spectrometer, by Waters Corporation (1 mentions)

Spelling variants of this product

Linear ion trap mass spectrometer (9 citations) LXQ mass spectrometer (6 citations) LXQ linear ion trap (3 citations) LXQ Ion Trap Mass Spectrometer (2 citations)

10 protocols using lxq linear ion trap mass spectrometer

Endoglycosidase-Mediated Antibody Modification

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Reactions were set up using 5 nM EndoS or EndoS mutants, or 100 nM EndoBT and 5 µM Rituximab or high-mannose-type IgG1 in PBS pH 7.4 at room temperature. Rituximab, a chimeric anti-human CD20 monoclonal antibody approved for treatment of B-cell lymphoma in adults, is produced in mammalian cell (Chinese Hamster Ovary) culture with the most abundant glycoforms being G0F, G1F, and G2F (antibody purchased from Premium Health Services, Inc.)^{57 (link)}. At various time intervals, 10 µl aliquots of the reaction were taken in duplicate and quenched with 1.1 µl of 1% trifluoroacetic acid. The quenched reaction was then mixed with 50 mM TCEP, and analyzed by LC-MS using an Accela LC System attached to a LXQ linear ion trap mass spectrometer (Thermo Scientific, Waltham, MA). Relative amount of the substrate and the hydrolysis products were quantified after deconvolution of the raw data and identification of the corresponding MS peaks using BioWorks (Thermo Scientific, Waltham, MA). The data were plotted in GraphPad Prism, and fit with a one-phase exponential decay curve.

Trastoy B., Klontz E., Orwenyo J., Marina A., Wang L.X., Sundberg E.J, & Guerin M.E. (2018). Structural basis for the recognition of complex-type N-glycans by Endoglycosidase S. Nature Communications, 9, 1874.

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Comprehensive Mass Spectrometry Analysis of PMP Degradation Products

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After PMP derivation (Section 2.4), the products of acid hydrolysis and photocatalytic degradation were analyzed by a LXQ linear ion trap mass spectrometer equipped with an electrospray ion source (ESI) and a PDA detector, controlled by XCalibur software (Thermo Fisher Scientific, Basel, Switzerland). The ESI-MS settings were set as we previously reported (Song et al., 2018 (link)). Data were acquired in positive mode (for acid hydrolysis samples) or negative mode (for photocatalytic degradation samples), and the scan range was set from m/z 100 to 2000 am. A TSKgel-Amide-80 (4.6 mm × 150 mm, 3 μm) column was used, the column temperature was 35 °C, and the mobile phase consisted of 20 mM ammonium acetate-acetonitrile (78:22, v/v, pH = 6.0) with a flow rate of 0.2 mL/min.

You Y., Song H., Wang L., Peng H., Sun Y., Ai C., Wen C., Zhu B, & Song S. (2021). Structural characterization and SARS-CoV-2 inhibitory activity of a sulfated polysaccharide from Caulerpa lentillifera. Carbohydrate Polymers, 280, 119006.

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HPLC and LC-MS Analysis of Carotenoids and Apocarotenoids

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HPLC analyses were carried out with an Agilent 1260 Infinity Quaternary HPLC system (Santa Clara, CA, USA) equipped with a pump (G1312C) with an integrated degasser (G1322A), a thermostatted column compartment (G1316A), an autosampler (G1329B), a diode-array detector (G1315D), and online analysis software (Chemstation). Analyses were performed at 25 °C using a normal-phase Zorbax Sil (5 µm, 4.6 × 150 mm) column (Agilent Technologies, Santa Clara, CA) protected with a guard column. Carotenoid and retinal separation was achieved using an isocratic composition of 70:30 (v:v) of hexane: ethyl acetate. The flow rate for all systems was 1.4 ml/min. Detection of carotenoids and apocarotenoids was performed at 420 nm wavelength. For LC-MS analyses, the eluate was directed into a LXQ linear ion trap mass spectrometer (Thermo Scientific) through atmospheric pressure chemical ionization (APCI) source working in the positive mode. To ensure optimal sensitivity, the instrument was tuned with Z as well as with retinal standards.

Babino D., Golczak M., Kiser P.D., Wyss A., Palczewski K, & von Lintig J. (2016). The biochemical basis of vitamin A3 production in arthropod vision. ACS chemical biology, 11(4), 1049-1057.

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Alanine Scan Mutants: Enzymatic Kinetics

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Reactions for the alanine scan mutants were set up using 100 nM EndoBT-3987_WT for reactions with RNAseB and 500 nM for reactions with high-mannose IgG1. The enzymes were mixed with 5 μM substrate in PBS pH 7.4 at room temperature. For the alanine scan, 10 μl aliquots of the reaction were taken in triplicate and allowed to progress for 30 and 45 min for RNAseB and high-mannose IgG1 substrates, respectively. All reactions were quenched using 1.1 μL of 1% trifluoroacetic acid. The quenched reactions were then mixed with 50 mM TCEP and analyzed by LC-MS using an Accela LC System attached to a LXQ linear ion trap mass spectrometer (Thermo Scientific, Waltham, MA). Relative amounts of the substrate and hydrolysis products were quantified after deconvolution of the raw data and identification of the corresponding peaks using BioWorks (Thermo Scientific, Waltham, MA). The data were plotted and statistical significance was determined using a multiple comparisons test (Tukey method) in GraphPad (GraphPad Software, LaJolla, CA).

Trastoy B., Du J.J., Klontz E.H., Li C., Cifuente J.O., Wang L.X., Sundberg E.J, & Guerin M.E. (2020). Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides. Nature Communications, 11, 899.

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Extraction and Quantification of Carotenoids

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Carotenoids and apocarotenoids were extracted from 100 μl of serum in 100 μl PBS or from 50 mg tissue homogenate in 200 μl PBS as previously described (26 (link)). In some analyses, lipids were saponified prior to extraction as described in (26 (link)). All HPLC analyses were performed on a normal-phase Zorbax Sil (5 μm, 4.6 × 150 mm) column. Chromatographic separation was achieved by isocratic flow (1.4 ml/min) of a mixture of ethyl acetate and hexane. For quantification of carotenoids and apocarotenoids, the HPLC column was scaled with known amounts of authentic standard substances. Mass spectrometry (MS)-based detection of 10,8’-diapocarotene-10,8’-dial was achieved with an LXQ linear ion trap mass spectrometer (Thermo Scientific, Waltham, MA) equipped with an atmospheric-pressure chemical ionization (APCI) interface coupled to an Agilent 1100 HPLC series (Agilent Technologies) and diode array detector (Agilent Technologies). The HPLC effluent was directed into the MS via an APCI probe operated in the positive ionization mode.

Kelly M.E., Ramkumar S., Sun W., Colon Ortiz C., Kiser P.D., Golczak M, & von Lintig J. (2018). The Biochemical Basis of Vitamin A Production from the Asymmetric Carotenoid β-Cryptoxanthin. ACS chemical biology, 13(8), 2121-2129.

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Rituximab Glycosylation Activity Assay

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Activity on fully glycosylated Rituximab was measured using 5 µM Rituximab with 1 µM AlfC_WT or AlfC_E274A in PBS for 1 month at 25 °C. Activity on partially deglycosylated Rituximab was measured using 5 µM Rituximab with 50 nM EndoS2 and 1 µM AlfC_WT in PBS overnight at 25 °C. EndoS2 rapidly hydrolyzes antibody glycans between the first and second N-acetylglucosamine residues, leaving one N-acetylglucosamine residue and fucose attached to each heavy chain of the antibody. After the designated incubation, 10 μl aliquots of each reactions were quenched by the addition of 1.1 μl trifluoroacetic acid. The quenched reactions were then mixed with 50 mM TCEP, and analyzed by LC–MS using an Accela LC System attached to an LXQ linear ion trap mass spectrometer (ThermoScientific, Waltham, MA), as previously described^{39 (link)}. Relative amounts of substrate and hydrolysis products were quantified after deconvolution of the raw data using BioWorks (ThermoScientific, Waltham, MA). Relative intensities by mass were then exported to GraphPad Prism and replotted, overlayed, and annotated.

Klontz E.H., Li C., Kihn K., Fields J.K., Beckett D., Snyder G.A., Wintrode P.L., Deredge D., Wang L.X, & Sundberg E.J. (2020). Structure and dynamics of an α-fucosidase reveal a mechanism for highly efficient IgG transfucosylation. Nature Communications, 11, 6204.

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Characterization of HDL oxidation

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HDL (200 μg/ml) was incubated with the NO donor, spermine NONOate (30 μM) in the presence or absence of homocysteine at 37°C in the absence or presence of 10μM copper for 16 hours. Oxidative reactions were terminated by the addition of DPTA. Five micrograms of HDL was lyophilized to dryness, and dissolved in 20 μl of 8 M urea/25 mM ammonium bicarbonate, pH 8.0, diluted further to lower urea concentration and digested with trypsin (1:50 protease to protein ratio) at 37°C for 4hours. The tryptic peptide pool was lyophilized to dryness, dissolved in 0.5% acetic acid, and analyzed by RP-HPLC-MS/MS on a Surveyor HPLC system and a 0.075 × 100 mm C18 RP column (Proxeon), at ≈1.5 μl/min, connected online via nano-electrospray with a LXQ linear ion trap mass spectrometer (ThermoFisher). Solvents were 99.5% water and 0.5% acetic acid (buffer A) and 90% acetonitrile, 9.5% water, and 0.5% acetic acid (buffer B). Peptides were eluted over a 90-min gradient from 5% to 60% solvent B and monitored by data dependent analysis MS/MS scans for the masses corresponding to tyrosine nitration and methionine oxidation (+45, +16 respectively).

Dias I.H., Polidori M.C., Li L., Weber D., Stahl W., Nelles G., Grune T, & Griffiths H.R. (2014). Plasma levels of HDL and carotenoids are lower in dementia patients with vascular comorbidities. Journal of Alzheimer's disease : JAD, 40(2), 399-408.

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Crosslinking and Mass Spectrometry of FliD

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FliD_78–405 crystals were crosslinked using 2% formaldehyde, harvested and washed in mother liquor, dissolved in water and the crosslinking reversed by heating the samples to 95°C for 20 min. The samples were analyzed by liquid chromatography (LC)-electrospray ionization (ESI)-mass spectrometry (MS) using a gradient of mobile phase A (0.1% formic acid in water) and mobile phase B (0.1% formic acid in acetonitrile) increasing from 0% B to 90% B in 20 min. The Accela LC System was attached to a LXQ linear ion trap mass spectrometer (Thermo Scientific). Raw MS data were analyzed using Xcalibus Qual Browser (Thermo Scientific) and deconvoluted using BioWorks (Thermo Scientific, Waltham, MA).

Postel S., Deredge D., Bonsor D.A., Yu X., Diederichs K., Helmsing S., Vromen A., Friedler A., Hust M., Egelman E.H., Beckett D., Wintrode P.L, & Sundberg E.J. (2016). Bacterial flagellar capping proteins adopt diverse oligomeric states. eLife, 5, e18857.

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S. aureus and S. epidermidis Lipid Analysis

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50 µg of the total lipids from S. aureus or S. epidermidis were dissolved in 100 µl of methanol. 10 ul of the methanol solution was loaded onto a nanospray tip for negative-mode ESI-MS and CID-MS using LXQ Linear Ion Trap Mass Spectrometer (Thermo Scientific). The spray voltage was set to 0.7 kV and the capillary temperature was set at 200 °C. For the CID-MS, collision energy was 20–30% of maximum and product ions were trapped with a q value of 0.25.

Fish D.N, & Abraham E. (1999). Pharmacokinetics of a Clarithromycin Suspension Administered via Nasogastric Tube to Seriously Ill Patients. Antimicrobial Agents and Chemotherapy, 43(5), 1277-1280.

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Mass Spectrometric Analysis of Bioactive Fractions

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Fractions B, C and D were analysed by mass spectrometry (MS) through electrospray ionization (ESI) obtained in a quadrupole time-of-flight (Q-TOF) mass spectrometer (Q-TOF2, Micromass, Manchester, UK) and fraction D was also analysed in an LXQ linear ion trap mass spectrometer (Thermo Scientific, San Jose, CA, USA). ESI-MS and MS/MS conditions in the Q-TOF mass spectrometer were the following: electrospray voltage was 3 kV in positive-ion mode with a cone voltage of 30 V; the source temperature was 80 C and the desolvation temperature was 150 C. Collision energy used for the MS/MS analysis varied between 30 and 40 eV. Data acquisition and treatment of results was carried out with the MassLynx™ software V4.0 (Waters, Manchester, UK). ESI-MS and MS/MS conditions used in the linear ion trap mass spectrometer were the following: electrospray voltage was 4.7 kV in negative-ion mode; capillary temperature was 275 C, and the sheath gas (He) flow rate was 25 units. For MS/MS acquisition, the normalized collision energy (CE) varied between 33 and 40 (arbitrary units). Data acquisition and treatment of results were carried out with the Xcalibur ® Data System 2.0 (Thermo Scientific, San Jose, CA, USA).

Castro A.R., Silva P.T.S., Castro P.J.G., Alves E., Domingues M.R.M, & Pereira M.A. (2018). Tuning culturing conditions towards the production of neutral lipids from lubricant-based wastewater in open mixed bacterial communities. Water research, 144.

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