Xcalibur v 4

Manufactured by Thermo Fisher Scientific

Sourced in United States

Xcalibur v.4.1 is a data analysis software for mass spectrometry instruments. It provides tools for data acquisition, processing, and reporting.

Automatically generated - may contain errors

Lab products found in correlation

Spelling variants of this product

Xcalibur (513 citations) Xcalibur 4.0 (226 citations)

22 protocols using xcalibur v 4

Determination of LOD and LOQ for L-Ala and L-Phe

Check if the same lab product or an alternative is used in the 5 most similar protocols

A total of 1 μM, 10 μM, 100 μM, 1 mM, and 10 mM of L-Ala or L-Phe, prepared from serial dilution, were incubated with 5 M urea in an aqueous solution for 2 d at 60 °C and pH 9. The reaction mixture with a total volume of 1 mL was incubated in a 1.5 mL Eppendorf tube. The resulting mixtures were subjected to LC-MS analysis. Each concentration point was conducted for three biological replicates. The response of the instrument (peak area) was plotted against the concentration of the calibration levels to give the standard curve. A linear regression model was applied to fit the data points, and the goodness of fit was evaluated using the correlation coefficient (R²). Within the linear range, R² should be greater than 0.99.
LOD and LOQ were calculated using the signal-to-noise ratio (S/N). LOD = 3 × (S/N); LOQ = 10 × (S/N). S/N values were obtained from the mass spectrometry data analysis software Xcalibur (v.4.1) (Thermo Scientific) and were calculated automatically when the peak area was integrated into the software.

Zhao R., Huang B., Lu G., Fu S., Ying J, & Zhao Y. (2023). A Practical Method for Amino Acid Analysis by LC-MS Using Precolumn Derivatization with Urea. International Journal of Molecular Sciences, 24(8), 7332.

+ Open protocol

+ Expand

Quantitative LC-MS/MS Dopamine Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

After reconstitution in 60% acetonitrile spiked with internal standards, samples were analysed using HPLC and triple-quadruple mass spectrometry and tandem mass spectrometry. Specifically, the system consisted of a TSQ system (Thermo Fisher Scientific) in line with an electrospray source and a Vanquish (Thermo Fisher Scientific) UHPLC consisting of a binary pump, degasser and auto-sampler outfitted with a XBridge Amide column (Waters; dimensions, 3.0 mm × 50 mm and a particle size of 3.5 μm). The mobile phase A contained 95% (v/v) water, 5% (v/v) acetonitrile, 10 mM ammonium hydroxide, 10 mM ammonium acetate, pH 9.0; B was 100% acetonitrile. The gradient was as follows: 0 min, 15% A; 3 min, 45% A; 10 min, 60% A; 10.1–11 min, 75% A; 11.1 min, 15% A; 11.1–15 min, 15% A with a flow rate of 150 μl min⁻¹. In positive/negative polarity switching mode, the capillary of the electrospray ionization source was set to 300 °C, with sheath gas at 35 arbitrary units, auxiliary gas at 5 arbitrary units and the spray voltage at 3.5 kV. The selective reaction of the protonated precursor ion and the related product ions were monitored. The transitions are listed as follows: dopamine (+) 154→137, dopamine_D4(+) 158→141. The peak area was integrated. Data acquisition and analysis were carried out using Xcalibur v.4.1 and Tracefinder v.4.1, respectively (both from Thermo Fisher Scientific).

González-Rodríguez P., Zampese E., Stout K.A., Guzman J.N., Ilijic E., Yang B., Tkatch T., Stavarache M.A., Wokosin D.L., Gao L., Kaplitt M.G., López-Barneo J., Schumacker P.T, & Surmeier D.J. (2021). Disruption of mitochondrial complex I induces progressive parkinsonism. Nature, 599(7886), 650-656.

+ Open protocol

+ Expand

Quantitative Metabolomics by HPLC-MS/MS

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Hydrophilic metabolites were analysed by HPLC–MS/MS as described previously^{71 (link)}. Briefly, 20–100 mg of weighed tissue was homogenized in 1 ml of cold methanol in the TissueLyzer, centrifuged and the equivalent volume for 10 mg of tissue was dried by SpeedVac, reconstituted in 50% acetonitrile and applied to the HPLC–MS/MS analysis. Data acquisition and analysis were carried out using Xcalibur v.4.1 and Tracefinder v.4.1 software, respectively (ThermoFisher Scientific). Metabolite concentrations within each sample were normalized to total ion count. Data are represented as log₂(fold change) relative to the control condition as indicated in the text and legends.

Levine D.C., Kuo H.Y., Hong H.K., Cedernaes J., Hepler C., Wright A.G., Sommars M.A., Kobayashi Y., Marcheva B., Gao P., Ilkayeva O.R., Omura C., Ramsey K.M., Newgard C.B., Barish G.D., Peek C.B., Chandel N.S., Mrksich M, & Bass J. (2021). NADH inhibition of SIRT1 links energy state to transcription during time-restricted feeding. Nature Metabolism, 3(12), 1621-1632.

+ Open protocol

+ Expand

Phenolic Compounds Quantification by HPLC-MS

Check if the same lab product or an alternative is used in the 5 most similar protocols

Phenolic compounds were quantified by Ultimate 3000 RSLC HPLC coupled with Orbitrap Fusion Mass Spectrometer (Thermo Fisher Scientific, Waltham, MA, United States). Chromatography separation was carried out by the Zorbax SB-Aq C18 column (250 mm × 4.6 mm, 5 μm, Agilent Technologies, Santa Clara, CA, United States). Meanwhile, the mobile phase is made up of 5% methanol with 0.1% formic acid (solvent A) and 0.1% formic acid in 100% methanol (solvent B). The initial mobile phase was 10% B maintained for 4 min before linearly increased to 80% within the next 11 min and maintained for 5 min. Then, the concentration of solvent B was linearly reduced to 10% within 10 min and maintained for 5 min. The flow rate was 600 μl/min, and the injection volume was 20 μl. Data were acquired in negative ESI mode using a spray voltage of 3,000 V, with sheath and aux gas set to 40 and 10, respectively, and also vaporizer and tube temperature set to 300 and 275°C. Data processing was accomplished using Xcalibur V4.1 (Thermo Fisher Scientific, Waltham, MA, United States).

Yi L., Wang Q., Luo H., Lei D., Tang Z., Lei S, & Xiao H. (2022). Bioactive Components From Gracilaria rubra With Growth Inhibition on HCT116 Colon Cancer Cells and Anti-inflammatory Capacity in RAW 264.7 Macrophages. Frontiers in Nutrition, 9, 856282.

+ Open protocol

+ Expand

Proteomic Analysis of Peptides via Orbitrap Fusion

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Depending on concentration, 0.5–2 μg of peptides were analyzed using Orbitrap Fusion Lumos mass spectrometer coupled with Dionex Ultimate 3000 RSLC Nano UHPLC (Thermo). After capturing on 2 cm long (0.2 mm internal diameter, 5 μm particle size) Acclaim PepMap 100 C18 trap column (Thermo) and washed with buffer A (0.1% formic acid) for 5 min at 5 μl min⁻¹, peptides were resolved on a 50 cm long (75 μm ID, 2 μm particle size) EASY-Spray column (Thermo) over a 80 min long gradient 2 to 32% buffer B (100% acetonitrile, 0.1% formic acid) at a flow rate of 0.2 μl min⁻¹, followed by a steep increase to 90% buffer B for 5 min and 5 min of step elution with 90% buffer B. Data collection was controlled with an XCALIBUR v.4.1 (Thermo). The data-dependent acquisition method was based on a published protocol^{32 (link)} except that each cycle was set to last for 2 s instead of 3 s.

Vasilyev N., Liu M.M., Epshtein V., Shamovsky I, & Nudler E. (2024). General transcription factor from Escherichia coli with a distinct mechanism of action. Nature Structural & Molecular Biology, 31(1), 141-149.

+ Open protocol

+ Expand

Quantification of Resveratrol Metabolites

Check if the same lab product or an alternative is used in the 5 most similar protocols

The metabolites were eluted with a Zorbax SB-Aq C18 column (Agilent Technologies, Santa Clara, CA, USA) at a flow rate of 0.6 ml/min. Mobile phase A was 5% acetonitrile in water, mobile phase B was 100% acetonitrile. Gradient elution started at 15% solvent B, linear gradient from 15 to 70% solvent B over 18 min, held at 70% B for 3 min, followed by washing and reconditioning the column. The Mass-spectra conditions were optimized at negative electrospray ionization mode, as follows: ion spray voltage 3.5 kv, ion transfer tube temperature 325°C, vaporizer temperature 275°C, sheath gas 15 Arb, aux gas 6 Arb, Orbitrap resolution 120K, and collision energy 30%. Data acquisition and processing were accomplished using Xcalibur V4.1 (Thermo Scientific, MA, USA).
The identified metabolites of RES were quantified by using the Shimadzu Model 2020 HPLC-MS (Shimadzu, Kyoto, Japan). The conditions of chromatography and Mass-Spectra were the same as those of Orbitrap Fusion HPLC-MS/MS. The data was processed with Labsolutions Software (Shimadzu, Kyoto, Japan).

Li F., Han Y., Wu X., Cao X., Gao Z., Sun Y., Wang M, & Xiao H. (2022). Gut Microbiota-Derived Resveratrol Metabolites, Dihydroresveratrol and Lunularin, Significantly Contribute to the Biological Activities of Resveratrol. Frontiers in Nutrition, 9, 912591.

+ Open protocol

+ Expand

Validation of Analytical Technique

Check if the same lab product or an alternative is used in the 5 most similar protocols

To monitor data quality and verify the reproducibility of the analysis, the performance of spiked injection and internal standards in all samples was validated and qualified as showing a relative standard deviation of less than 10%. Xcalibur v.4.1 software (Thermo Fisher Scientific) was used for data acquisition and peak integration analysis. All data were normalized using the lowest tissue biopsy weight (1.8 mg).

Yazd H.S., Bazargani S.F., Vanbeek C.A., King-Morris K., Heldermon C., Segal M.S., Clapp W.L, & Garrett T.J. (2021). LC-MS lipidomics of renal biopsies for the diagnosis of Fabry disease. Journal of Mass Spectrometry and Advances in the Clinical Lab, 22, 71-78.

+ Open protocol

+ Expand

PFAS Quantification by LC-MS/MS

Check if the same lab product or an alternative is used in the 5 most similar protocols

Data acquisition and peak integration were performed using Xcalibur v.4.1 software (Thermo-Fisher Scientific). SRM transitions were used to detect and quantify PFAS, with the most intense transition used to quantify the PFAS while the second transition was used to confirm the identification (if applicable). For non-labeled PFAS without a labeled analogue, an alternative labeled standard closely related by structure and/or retention time was used. Table S1 summarizes the PFAS and respective IS used for quantification. A linear regression model was used to build the calibration equation for each PFAS, and the intercept, slope and correlation coefficient r² were calculated. A total sum of isomers is presented for perfluorohexanoic acid (PFHxS) and PFOS (as ΣPFHxS and ΣPFOS, respectively), as these compounds were monitored as isomeric mixtures in the calibration curves. Extraction recovery was investigated by comparison of the peak area of the replicates of the pooled samples spiked before and after SPE extraction (shown as %). Method detection and quantification limits were defined as the minimum concentration that would yield (visually) a detectable chromatographic peak with signal-to-noise ratio of 3 (S/N > 3) and a S/N > 10 for limit of quantification (LOQ).

da Silva B.F., Aristizabal-Henao J.J., Aufmuth J., Awkerman J, & Bowden J.A. (2022). Survey of per- and polyfluoroalkyl substances (PFAS) in surface water collected in Pensacola, FL. Heliyon, 8(8), e10239.

+ Open protocol

+ Expand

UPLC-MS Analysis of Compound Mixtures

Check if the same lab product or an alternative is used in the 5 most similar protocols

Samples were separated and analyzed by a UPLC/MS system including the Dionex^® UltiMate 3000 RSLC ultrahigh-pressure liquid chromatography system, with a workstation with Thermo Fisher Scientific’s Xcalibur v. 4.0 software package (Waltham, MA, USA). After the photodiode array detector, the eluent flow was guided to a Q Exactive Plus Orbitrap high-resolution high-mass-accuracy mass spectrometer (MS). Mass detection was a full MS scan with low-energy collision-induced dissociation (CID) from 100 to 1000 m/z in positive-ionization mode with an electrospray (ESI) interface. The mass resolution was 140,000. Substances were separated on a PhenomenexTM Luna C8 reverse phase column.

Cho E., Gurdon C., Zhao R., Peng H., Poulev A., Raskin I, & Simko I. (2023). Phytochemical and Agronomic Characterization of High-Flavonoid Lettuce Lines Grown under Field Conditions. Plants, 12(19), 3467.

+ Open protocol

+ Expand

Analytical Data Processing and Visualization

Check if the same lab product or an alternative is used in the 5 most similar protocols

Data was analyzed in XCalibur v4.0 and/or Tracefinder v4.1 (Thermo). Statistical analysis and graph generation was conducted in GraphPad Prism v7.04 (GraphPad Software La Jolla, CA).

Kuskovsky R., Buj R., Xu P., Hofbauer S., Doan M.T., Jiang H., Bostwick A., Mesaros C., Aird K.M, & Snyder N.W. (2018). Simultaneous isotope dilution quantification and metabolic tracing of deoxyribonucleotides by liquid chromatography high resolution mass spectrometry. Analytical biochemistry, 568, 65-72.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!