Data were collected using the Thermo Xcalibur 2.2 software (Thermo Scientific, San Jose, USA) and edited with Microsoft Excel (2007). Continuous variables were expressed by mean ± standard deviation (‾x ± sd), and non-normal distribution was represented by M (P25, P75). Comparison of means between groups was performed using independent samples T-test for normally distributed data and Mann–Whitney U-test for non-uniformly distributed data. Categorical variables are presented as N (%) and compared using the chi-square test or Fisher exact test. The Simca-P software (version 11.0; Umetrics, Sweden) was used to perform partial least squares discriminant analysis (PLS-DA). The false discovery rate (FDR) was used for multiple testing adjustment. Pathway enrichment analysis of differential metabolites was performed using a hypergeometric test and topological analysis with the aid of the online database KEGG (Kyoto Encyclopedia of Genes and Genomes, www.kegg.jp/kegg/kegg1.html ) pathway analysis. Bioinformatics analysis of differential metabolites was conducted using ingenuity pathway analysis (IPA) software. Clinical data were analyzed using SPSS Statistics 25 (version 25.0.0.1, IBM, USA). Statistical significance was set at P < 0.05.
Thermo xcalibur 2
Manufactured by Thermo Fisher Scientific
Sourced in United States, Germany
Thermo Xcalibur 2.1 is a software package for data acquisition, analysis, and management in mass spectrometry applications. It provides a unified platform for instrument control, data processing, and reporting.
Automatically generated - may contain errors
Lab products found in correlation
Acquity beh c18 column, by Waters Corporation (2 mentions)
Ultimate 3000 rslcnano system, by Thermo Fisher Scientific (2 mentions)
Metworks version 1.3, by Thermo Fisher Scientific (2 mentions)
Mass frontier version 8.0, by Thermo Fisher Scientific (2 mentions)
Simca p software, by Sartorius (1 mentions)
Spss statistics 25, by IBM (1 mentions)
Peakview1, by AB Sciex (1 mentions)
Surfacelab 7, by ION-TOF (1 mentions)
Q exactive hybrid quadrupole orbitrap mass spectrometer, by Thermo Fisher Scientific (1 mentions)
Easy spray nano electrospray ion source, by Thermo Fisher Scientific (1 mentions)
Masslynx software, by Waters Corporation (1 mentions)
Spss v17, by IBM (1 mentions)
Spss software package version 19, by IBM (1 mentions)
Liquid chromatography system, by Waters Corporation (1 mentions)
Synapt g2 hdms quadrupole time, by Waters Corporation (1 mentions)
Beh c18 column, by Waters Corporation (1 mentions)
Simca 14, by Sartorius (1 mentions)
Dionex ultimate 3000 hplc system, by Thermo Fisher Scientific (1 mentions)
Q exactive mass spectrometer, by Thermo Fisher Scientific (1 mentions)
Acquity uplc, by Waters Corporation (1 mentions)
21 protocols using thermo xcalibur 2
1
Metabolomic Analysis of Differential Metabolites
2
Quantitative Analysis of Menaquinones
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Menaquinones were analyzed using UHPLC-ESI-MS operated on the positive ion mode. The sample was resolved on an Acquity BEH C18 column (150 mm × 2.1 mm, 1.8 μm) supplied by Waters, Milford, MA, USA. Flowrate was 0.5 ml/min at 30 °C. The mobile phase consisted of solvent A (0.1% formic acid in water) and solvent B (0.1% formic acid in acetonitrile). Chromatographic separation was 6-min. The gradient was 0 min, 8% B; 1 min, 8% B; 4.3 min, 25% B; 5 min, 8% B; 6 min, 8% B. The detection was by means of diode-array which was set up at 248 nm. The method of ionization was electrospray ionization (ESI). The cone voltage was set to 30 V, the source temperature at 147 °C; the desolvation gas flow was 483 L/h at a temperature of 300 °C.
The data acquisition and processing was obtained using Thermo Xcalibur 2.2 software (Thermo Fisher Scientific, U.S.A).
The data acquisition and processing was obtained using Thermo Xcalibur 2.2 software (Thermo Fisher Scientific, U.S.A).
3
Metabolomics Analysis by UHPLC-Q-TOF-MS/MS
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The data collected via UHPLC-Q-TOF-MS/MS were processed using Peak View 1.2 software (AB SCIEX, version 1.2.0.3) from AB Sciex Company. The empirical molecular formulae were deduced from Peakview by comparing the theoretical masses of molecular ions and/or adductions with the determined values based on the following error limits: mass accuracy, < 5 ppm; retention time, < 5.0%; and isotope abundance, < 10%. The multistage mass spectrometry data collected via ESI-LTQ-Orbitrap-MSn were processed using Thermo Xcalibur 2.2 (Thermo Fisher Scientific).
4
Nano-DESI Mass Spectrometry for Metabolite Analysis
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A nano-DESI source was interfaced with a Thermo Finnigan LTQ XL linear ion trap mass spectrometer (Mountain View, CA, USA), as shown in Figure 1 c. The lateral and vertical positions of the liquid junction were adjusted by the XYZ-positioning stage (Newport, San Jose, CA, USA) and monitored by two video cameras. Mass spectra were recorded in the negative ion mode using the full scan mode, SIM mode, or pSRM mode. The spray and capillary voltages were set to −5 kV and −10 V, respectively. For the pSRM mode acquisition, product ions were generated via collision-induced dissociation at a normalized collision energy of 30% or 35%. Mass spectral raw data were first processed by Thermo Xcalibur 2.2 (Thermo Fisher Scientific, Waltham, MA, USA) to generate mass spectra and ion chronograms. The generated mass spectra were further processed by mMass version 5.5 (http://www.mmass.org , accedded on 20 September 2022) for data presentation.
5
Mass Spectrometry Imaging Data Analysis
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TOF-SIMS data
analysis was performed using SurfaceLab 7 (IONTOF GmbH, Germany).
MALDI-MSI data were analyzed using Thermo Xcalibur 2.2 and Thermo
ImageQuest (Thermo-Fisher Scientific, USA), METASPACE (https://metaspace2020.eu ), and
LipostarMSI (Molecular Horizons Srl, Italy). All images were normalized
to total ion count (TIC) and denoised by hotspot removal. Segmentation
(bisecting K-means algorithm), colocalization, and PCA analyses were
performed using LipostarMSI.
analysis was performed using SurfaceLab 7 (IONTOF GmbH, Germany).
MALDI-MSI data were analyzed using Thermo Xcalibur 2.2 and Thermo
ImageQuest (Thermo-Fisher Scientific, USA), METASPACE (
LipostarMSI (Molecular Horizons Srl, Italy). All images were normalized
to total ion count (TIC) and denoised by hotspot removal. Segmentation
(bisecting K-means algorithm), colocalization, and PCA analyses were
performed using LipostarMSI.
6
Peptide Identification Using Nano-LC-MS/MS
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The peptides were identified using an UltiMate® 3000 RSLCnano system (Thermo Fisher Scientific, USA) coupled with Q Exactive Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific, USA) through EASY-Spray nano-electrospray ion source (Thermo Fisher Scientific, USA). The samples were loaded with 5–7% Acetonitrile (ACN) in 5 min, 7–45% in 60 min, 45–50% in 5 min, and 50–97% in 5 min, followed by washing at 100% at 300 nL/min flow rate for 90 min. Full MS scan was carried with mass ranges of m/z 200–2000. Precursor ions with + 1 and greater than + 8 charge state were excluded. Fragmentation of precursor ions was performed using Higher-energy collisional dissociation and data acquisition was performed by Thermo Xcalibur 2.2 (Thermo Fisher Scientific, USA).
7
Cornea Metabolite Extraction and Analysis
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The cornea of each denervated and control mouse was homogenized in an extract buffer (water/methanol, 1:3 vol/ vol) and in a mixed internal standard application liquid. After centrifugation, the supernatant was evaporated to dryness under vacuum. A sodium bicarbonate buffer (0.2 M, pH 11) and dansyl chloride in acetone (2 mg/mL) were then added to the dry residues for derivatization. The sample or standard substance was injected into ultra-high performance liquid chromatography-electrospray ionization-tandem mass spectrometry and the data were analyzed by software (Thermo Xcalibur 2.2; Thermo Fisher Scientific, Waltham, MA, USA).
8
Fatty Acid Identification Protocol
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The entire list of centroid peaks with collected information (e.g., retention times, m/z values, peak intensities) was exported from Thermo Xcalibur 2.1 Software (Thermo Fisher Scientific, Inc., Waltham, MA, USA). Retention time (RT) was calibrated by retention indices (RIs) as reported [28] to overcome the drifting of retention times. Peak pair extraction was operated with 4.025 Da mass difference, similar peak intensities, and RIs by using in-house MATLAB-based software. Prospective molecular formulas of DMED-labeled fatty acids were generated based on the accurate m/z using the Thermo Xcalibur 2.1 Software. Mass tolerance of 5.0 mDa was set, and the elements C, H, N, and O were used. Based on accurate mass and retention time, positive fatty acid identification was performed using an in-house chemically labeled standard library (http://59.110.238.58/search ).
9
Structural Analysis of Cationized PTX, 3p-OHP, and 6α-OHP
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Tandem MS experiments of cationized PTX, 3p-OHP and 6α-OHP ions were performed on a Thermo Scientific Q-Exactive hybrid quadrupole-Orbitrap mass spectrometer (Q-Orbitrap instrument, Thermo Scientific, San Jose, CA, USA) in positive ion mode. Samples were injected with a syringe pump at a flow rate of 5 μL/min, and the electrospray voltage and capillary temperature were set as 3.0 kV and 200°C, respectively. Spectra of all samples were acquired over 200 scans and averaged, and the peaks were analyzed using Thermo Xcalibur 2.1 software (Thermo Scientific). The 20% of the normalized collision energy was applied to all analyte ions. Additional tandem MS experiments were performed on the Synapt G2 HDMS instrument along with the IM separation in positive ion mode at the trap (CID-IM-MS) and the transfer cell (IM-CID-MS), which were placed before and after the IM cell, respectively. Spectra of all samples were acquired over 200 scans and averaged, and the peaks were analyzed using MassLynx software (ver. 4.1, Waters, Milford, MA, USA). Forty eV of collision energy was applied to all analyte ions, and the other parameters were the same to the IM-MS experiments without tandem MS.
10
High-Resolution Mass Spectrometry Analysis of Daidzein Metabolites
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A Thermo Xcalibur 2.1 workstation (Thermo Scientific) was adopted for acquiring and processing HR-ESI-MS1 and MSn data. To obtain as many product ions of daidzein metabolites as possible, the peaks detected with intensity over 10,000 for negative ion mode and 50,000 for positive ion mode were selected for further structural characterization. The chemical formula for all parent ions were calculated from accurate mass using a formula predictor with the parameters set as followings: C [6–35], H [5–50], O [0–15], S [0–5], N [0–5], and ring double bond (RDB) equivalent value [0–15]. Meanwhile, MetWorks (Version 1.3) and Mass Frontier (Version 8.0) software (Thermo Scientific, Waltham, MA, USA) were utilized for mass fragmentation behaviors analysis, structural elucidation, and chromatographic peaks extraction.
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