Xcalibur software

Manufactured by Thermo Fisher Scientific

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Xcalibur is a software package developed by Thermo Fisher Scientific for the control and management of mass spectrometry instrumentation. It provides a comprehensive suite of tools for data acquisition, processing, and analysis. The software's core function is to enable users to operate and interact with Thermo Fisher Scientific's mass spectrometry systems.

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Xcalibur (513 citations) Thermo Xcalibur software (46 citations) Xcalibur software v2.1 (15 citations) Xcalibur software version 4.0 (13 citations) Xcalibur software package (11 citations) Xcalibur software version 3.0 (8 citations) Thermo Xcalibur Qual Browser software (8 citations) Xcalibur acquisition software (5 citations) Xcalibur software v4.0 (4 citations) Xcalibur quantitative software (3 citations)

740 protocols using xcalibur software

Quantitative Analysis of Intra-Articular Anesthetics

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Chromatographic data analysis (Xcalibur^TM software version 2.2 SP1, Thermo Fischer, Waltham, Mass.) and calculation of calibration curves (and linearity check) (Prism version 9 for MacOS, Graphpad software, San Diego, California) was performed using commercially available statistical software programs (Xcalibur^TM software version 2.2 SP1, Thermo Fischer, Waltham, Mass. and Prism version 9 for MacOS, Graphpad software, San Diego, California). The statistical software was chosen because of the option to estimate confidence intervals for predicted (back calculated) concentrations.
Summary statistics (mean and standard deviation) were used for the presentation of concentrations of mepivacaine and lidocaine measured in SF of specific joints after intra-articular injection (Tables 1, 2) and calculated using GraphPad Prism. Similarly, data per joint and time point was tested for normality using Shapiro-Wilk test in GraphPad Prism.

Adler D.M., Jørgensen E, & Cornett C. (2022). The concentration of lidocaine and mepivacaine measured in synovial fluid of different joints of horses after single intra-articular injection. Frontiers in Veterinary Science, 9, 1007399.

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Saikosaponin Quantification in Radix Bupleuri

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The peak areas in TIC of the detected saikosaponins were integrated automatically using Qual Browser in Xcalibur software (version 2.2 SP1.48, Thermo Fisher Scientific Inc, San Jose, CA, USA). The saikosaponin contents were calculated by substituting the peak areas into the established calibration curve equations. Each Radix Bupleuri sample was quantitatively analyzed in triplicate. The saikosaponin contents were expressed as mean and standard deviation and subjected to analysis of variance (ANOVA) and box-plot analysis using OriginPro software (version 9.1, OriginLab Corporation, Northampton, MA, USA). HPLC-MS and GC-MS data were recorded automatically by Xcalibur software and processed by SIEVE software (Version 2.1, Thermo Fisher Scientific Inc., San Jose, CA, USA) for peak matching, peak alignment, and peak area normalization. Additionally, a data table containing sample name, retention time, m/z, and peak intensity was obtained. Data from isotope peaks and missing values greater than 80% were removed. The remaining data were imported into SIMCA-P software (Version 14.1, Umetrics, Umeå, Sweden) and converted for multivariate statistical analysis, including PCA, HCA, and PLS-DA.

Wang Z., Zhao H., Tian L., Zhao M., Xiao Y., Liu S, & Xiu Y. (2022). Quantitative Analysis and Differential Evaluation of Radix Bupleuri Cultivated in Different Regions Based on HPLC-MS and GC-MS Combined with Multivariate Statistical Analysis. Molecules, 27(15), 4830.

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Automated Nanoelectrospray for FT-MS Analysis

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Sample preparation. The sample was 1/2 diluted with ACN + 1% formic acid.
MS Conditions. Mass Spectrometer: LTQ-FT Ultra (Thermo Fisher Scientific, Waltham, MA, USA). Sample introduction: Direct infusion (Automated Nanoelectrospray). The NanoMate (Advion BioSciences, Ithaca, NY, USA) aspirated the samples from a 384-well plate (protein Lobind) with disposable, conductive pipette tips, and infused the samples through the nanoESI Chip (which consists of 400 nozzles in a 20 × 20 array) into the mass spectrometer. Spray voltage was 1.70 kV and delivery pressure was 0.50 psi. Other conditions were as follows: nanoESI, positive ionization was used, m/z range: 100–2000 amu, capillary temperature: 200 °C, capillary voltage: 35 V, tube lens: 100 V.
Data Processing. Data was acquired with Xcalibur software, version 2.0 SP2 (Thermo Fisher Scientific, Waltham, MA, USA). Elemental compositions from experimental exact mass monoisotopic values were obtained with a dedicated algorithm integrated into Xcalibur software (2.0 SP2, Thermo Fisher Scientific, Waltham, MA, USA).

Kalafatovic D., Mauša G., Rešetar Maslov D, & Giralt E. (2020). Bottom-Up Design Approach for OBOC Peptide Libraries. Molecules, 25(15), 3316.

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Quantification of Clozapine in Rat Serum

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Serum was isolated from procoagulated whole blood, collected over 24 h from the tail vein or via cardiac puncture (endpoint only), by centrifugation at 10,000× g for 10 min at 4 °C. Clozapine serum samples were combined with methanol and internal standard carbamazepine (0.5 μg/mL, 1.5 μM), Clozapine standards were prepared in methanol (0.01−2.0 μg/mL, 0.03 μM−6.1 μM), combined with internal standard carbamazepine (0.5 μg/mL, 1.5 μM), and blank rat serum. Serum proteins were precipitated for >1 h at −20 °C, and supernatants were isolated following centrifugation at 16,000× g for 10 min. Clozapine drug levels were measured using a TSQ Altis Triple Quadrupole Mass Spectrometer (Thermo Fisher, Waltham, MA, USA) interfaced with a 1260 Infinity II Prime LC System (Agilent Technologies, Santa Clara, CA, USA) and analyzed using XCalibur software (Thermo Fisher, Waltham, MA, USA). The mobile phase consisted of 60% aqueous (0.1% formic acid, 1 mM ammonium formate in H₂O) and 40% organic (acetonitrile), and a Poroshell 120 EC-C18, 3.0 × 50 mm, 2.7 μm column (Agilent Technologies, Santa Clara, CA, USA) was employed. Quantification was performed using XCalibur software (Thermo Fisher, Waltham, MA, USA) (Figure 9).

Sernoskie S.C., Jee A, & Uetrecht J. (2023). The Role of Myeloperoxidase in Clozapine-Induced Inflammation: A Mechanistic Update for Idiosyncratic Drug-Induced Agranulocytosis. International Journal of Molecular Sciences, 24(2), 1243.

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LC-MS/MS Quantification of Midazolam and Metabolite

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All measurements were performed using an LC-MS/MS system in the selective reaction monitoring (SRM) mode. A Triple Stage Quadrupole Vantage mass spectrometer an HESI-II spray source coupled to an Accela™ LC system (Thermo Fisher Scientific, Waltham, MA, USA) was employed. The vaporizer and capillary temperatures were set to 150°C and 300°C, respectively. Electrospray ionization was performed in the positive mode at a spray voltage of 3500 V. Nitrogen was used as the sheath and auxiliary gas, and was set to 45 and 20 (arbitrary units), respectively. Data were analyzed using the Xcalibur software (Thermo Fisher Scientific). An ACE^® 5C18 column (5 μm, 50 mm × 2.1 mm, Advanced Chromatography Technologies, Scotland, UK) and a guard C18 column (2 μm, 2.1 mm ID, Phenomenex, Torrance, CA, USA) were employed for LC separation. The mobile phase consisted of ACN with 0.1% FA (mobile phase A) and water (mobile phase B) at a flow rate of 220 μL/min. The gradient was as follows: 0 minute 5% A, 0.5 minutes 5% A, 1.5 minutes 95% A, 3.0 minutes 95% A, 3.5 minutes 5% A, 5.0 minutes 5% A. Ions monitored in the SRM mode were m/z 326.0→291.0 for MDZ, 342.0→203.0 for 1’-OH-MDZ m/z, and 609.4→174.1 for the IS, respectively, at an SRM collision energy of 29 eV for MDZ, 15 eV for 1ʹ-OH-MDZ and 42 eV for IS. Data procurement was controlled using the Xcalibur software (Thermo Fisher Scientific).

Jo J.H., Kim S.J., Nam W.S., Seung E.J, & Lee S. (2016). Decreased absorption of midazolam in the stomach due to low pH induced by co-administration of Banha-sasim-tang. Environmental Health and Toxicology, 31, e2016016.

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Quantification of Aflatoxins by LCMSMS

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The system consisted of two pumps (LC-10ADvp, Shimadzu, Toyoto, Japan), an on-line degasser (DGU-12A, Shimadzu), and a triple quadrupole mass spectrometer equipped with a heated ESI source (TSQ Quantum, Thermo Scientific, San Jose, CA, USA). Both the LC and mass spectrometer were controlled by Xcalibur software (Thermo Finnigan). A C₁₈ reversed-phase column (Ascentis^® 3 μm particle size, 10cm × 2.1 mm, Sigma-Aldrich Chemicals, St, Louise, USA) was used for separation. MeOH/Water mixture (60/40, v/v) containing 5mM ammonium acetate was used as the mobile phase at a flow rate of 0.150 mL/min. Sample injection volume was 5 μL. Data was acquired in full scan and SRM mode. The MS detector was operated in the positive ion mode with the following settings: spray voltage 3 KV, vaporization temperature 270 °C, capillary temperature 300°C, sheath gas pressure 35 (arb), auxiliary gas pressure 10 (arb), tube lens voltage of 150 V, and capillary voltage of 35 V, respectively. SRM parameters for MS detection of aflatoxins are summarized in Table 1.

McCullum C., Tchounwou P., Ding L.S., Liao X, & Liu Y.M. (2014). Extraction of Aflatoxins from Liquid Foodstuff Samples with Polydopamine-Coated Superparamagnetic Nanoparticles for HPLC-MS/MS Analysis. Journal of Agricultural and Food Chemistry, 62(19), 4261-4267.

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Quantification of Analytes via UPLC-MS

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A Waters ACQUITY UPLC system (Waters Corporation, Milford, MA, USA), coupled with a tandem MS (Finnigan TSQ Quantum Ultra triple-quadrupole MS, Thermo Electron, San Jose, CA, USA), in combination with the Xcalibur software (Thermo-Finnigan, Bellefonte, PA, USA) was used to detect and quantify analytes. The LC–MS system was equipped with an electrospray ion source and ran in negative mode. The injection volume was 10 μL on an ACQUITY UPLC CSH Phenyl-Hexyl column (130 Å, 1.7 µm, 2.1 mm × 100 mm, Waters Corporation, Milford, MA, USA) equipped with a filter (Waters Acquity UPLC™ BEH C18 column, 1.7 μm, 2.1 mm × 5 mm) in front of the column. The flow rate was 300 μL/min, and the column temperature was 40 °C. Solvents were 0.1% acetic acid in water (A) and 0.1% acetic acid in acetonitrile (B).

Chen Y.C., Chen H.J., Huang B.M., Chen Y.C, & Chang C.F. (2019). Polyphenol-Rich Extracts from Toona sinensis Bark and Fruit Ameliorate Free Fatty Acid-Induced Lipogenesis through AMPK and LC3 Pathways. Journal of Clinical Medicine, 8(10), 1664.

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Quantifying Phthalate Metabolites in Breast Milk

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Phthalate metabolites in human breast milk were measured using a Waters ACQUITY UPLC system (Waters Corporation, Milford, MA, USA) coupled with tandem MS (Finnigan TSQ Quantum Ultra triple-quadrupole MS, Thermo Electron, San Jose, CA, USA) in combination with Xcalibur software (ThermoFinnigan, Bellefonte, PA, USA). The LC–MS–MS system was equipped with an electrospray ion source (ESI) and was run in negative mode. The injection volume was 10 μL on an ACQUITY UPLC CSH Phenyl-Hexyl Column (130 Å, 1.7 µm, 2.1 × 100 mm, Waters Corporation, Milford, MA, USA) equipped with a filter (Waters Acquity UPLC™ BEH C18 column, 1.7 μm, 2.1 × 5 mm) in front of the column. The flow rate was 250 μL/min, and the column temperature was 40 °C. Solvents were A: 0.1% acetic acid in water and B: 0.1% acetic acid in acetonitrile. Solvent programming was 0.0–5.0 min, 30% B; 10.0 min, 40% B; 12.0 min, 50% B; 13.0 min, 100% B; and 13.1–15.0 min, 10% B. The limit of detection (LOD), limit of quantitation (LOQ), and linear range of standard curves for phthalate metabolites are summarized in Supplementary Table S1. The analyzed phthalate metabolites included mono-2-ethylhexyl phthalate (MEHP), mono-(2-ethyl-5-carboxypentyl) phthalate (MECPP), mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP), mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP), mono[2-(carboxymethyl)hexyl] phthalate (MCMHP), MBzP, MiBP, and MBP.

Hung S.C., Lin T.I., Suen J.L., Liu H.K., Wu P.L., Wu C.Y., Yang Y.C., Yang S.N, & Yang Y.N. (2021). Phthalate Exposure Pattern in Breast Milk within a Six-Month Postpartum Time in Southern Taiwan. International Journal of Environmental Research and Public Health, 18(11), 5726.

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Peptide Identification by LC-MS/MS

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Samples were analyzed by LC-MS/MS using a Q Exactive™ Orbitrap mass spectrometer (Thermo Scientific) coupled online with a RSLC nano-HPLC (Ultimate 3000, Thermo Scientific) to derive mass spectra of individual peptides and peptide fragment ions were identified with tandem mass spectrometry (MS/MS). Samples were injected onto a Thermo RSLC pepmap100, 75 um id, 100 Å pore size, 50 cm reversed phase nano column with 95% buffer A (0.1% formic acid) at a flow rate of 300 nL/min. The peptides were eluted over a 60-min gradient to 40% buffer B (80% Acetonitrile 0.1% formic acid). The eluate was nebulised and ionized using the Thermo nano electrospray source coated silica emitter with a capillary voltage of 1700 V. Peptides were selected for MS/MS analysis using Xcalibur software (Thermo Finnigan) in Full MS/dd-MS² (TopN) mode with the following parameter settings: TopN 10, MSMS AGC target 5e4, 120 ms Max IT, NCE 27 and 2 m/z isolation window. Dynamic exclusion was set to 30 s. Generally a single injection was performed for each experimental preparation replicate and two blank injections between each experimental sample.

Rees M.A., Stinear T.P., Goode R.J., Coppel R.L., Smith A.I, & Kleifeld O. (2015). Changes in protein abundance are observed in bacterial isolates from a natural host. Frontiers in Cellular and Infection Microbiology, 5, 71.

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Quantification of Circulating PCS Levels

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We obtained a standard sample of PCS from Alsachim (Illkirch-Graffenstaden, France). The measurement of circulating PCS levels were described in detail previously [6 (link)]. Samples containing mixtures of PCS were analyzed with the UHPLC through the Accela 1250 autosampler and separated by a Shiseido HPLC CAPCELL PAK C18 MGII column (150 mm x 1.5 mm, 3.0 μm, Tokyo, Japan). The multiple reaction monitoring (MRM) scanning mode was applied for quantification. We used the Xcalibur software (version 2.2, Thermo-Finnigan Inc., San Jose, CA, USA) to acquire the MS spectra and control the mass spectrometer.

Chang J.F., Hsieh C.Y., Liou J.C., Lu K.C., Zheng C.M., Wu M.S., Chang S.W., Wang T.M, & Wu C.C. (2021). Circulating p-Cresyl Sulfate, Non-Hepatic Alkaline Phosphatase and Risk of Bone Fracture Events in Chronic Kidney Disease-Mineral Bone Disease. Toxins, 13(7), 479.

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