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Xcalibur qualbrowser 4

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The XCalibur QualBrowser 4.0.27.10 is a software tool designed for the analysis and interpretation of mass spectrometry data. It provides a user-friendly interface for visualizing and processing complex data sets generated by Thermo Fisher Scientific mass spectrometry instruments.

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Lab products found in correlation

Q exactive hf mass spectrometer with extended mass range qe emr, by Thermo Fisher Scientific (2 mentions) Q exactive hf ultra high mass range qe uhmr, by Thermo Fisher Scientific (2 mentions) Prism 5, by GraphPad (1 mentions) Prism 9, by GraphPad (1 mentions) Prism 8, by GraphPad (1 mentions) Q exactive hf mass spectrometer, by Thermo Fisher Scientific (1 mentions)

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Xcalibur 4.0 Xcalibur

7 protocols using xcalibur qualbrowser 4

1

Mycotoxin Quantification via UPLC-MS

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Use Thermo Xcalibur Qual Browser 4.0 to recognize UPLC-MS raw data. Mycotoxin recoveries for each solvent mixture and purification method were evaluated using two-way ANOVA at a significance level of 0.05; Tukey’s multiple comparisons testing was used to evaluate the significance of difference within each group. GraphPad Prism 5.0 software is used for all statistical analysis and graphic production.
Zhou H., Yan Z., Yu S., Wu A, & Liu N. (2022). Development of a Novel UPLC-MS/MS Method for the Simultaneous Determination of 16 Mycotoxins in Different Tea Categories. Toxins, 14(3), 169.
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2

Determination of Mycotoxins in Wheat Flour

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The UPLC-MS raw data were recognized by Thermo Xcalibur Qual Browser 4.0. Nonparametric statistics were used after the normality and lognormality testing for each group. Distribution characteristics and differences of mycotoxins in various types of wheat flour samples were compared and evaluated using the Kruskal-Wallis or Mann-Whitney test at a significance level of 0.05. All statistical analyses and drawings were performed using GraphPad Prism 9.0 software.
Zhou H., Xu A., Liu M., Yan Z., Qin L., Liu H., Wu A, & Liu N. (2022). Mycotoxins in Wheat Flours Marketed in Shanghai, China: Occurrence and Dietary Risk Assessment. Toxins, 14(11), 748.
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3

Quantitative Proteomics and Glycomics of Viral Spike Proteins

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For the proteomics experiment, data collected was submitted to MaxQuant for protein identification and quantitation. Proteins were searched against SARS-CoV S protein, SARS-CoV-2 S protein, MERS S protein and human proteome UP000005640. The identification FDR was 0.01. The MaxQuant score was set to 60. The assignment of glycoproteins was based on UniprotKB. The abundance of viral spike proteins relative to human proteins were calculated. Human glycoproteins which might affect the quantitation of viral spike protein N-glycans were investigated.
For glycomics experiment, acquired .raw files were processed Skyline (MacCoss Lab Software) with in-house glycan library. All possible m/z values of each glycan adduct forms were evaluated manually. Relative quantitation of glycans was performed using Microsoft Excel. Chromatograms and MS2 spectra were generated with Skyline and XCalibur Qual Browser 4.3 (Thermo Scientific). MS2 spectra were carefully examined with GlycoWorkbench 2. Other figures were made with GraphPad Prism 8.4.3. Workflow scheme was made with biorender.com.
Cho B.G., Gautam S., Peng W., Huang Y., Goli M, & Mechref Y. (2021). Direct comparison of N-glycans and their isomers derived from spike glycoprotein 1 of MERS-CoV, SARS-CoV-1 and SARS-CoV-2. Journal of proteome research, 20(9), 4357-4365.
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4

Blinded LC-MS Analysis of Pharmacological Treatments

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LC-MS data were collected and processed using Thermo Xcalibur Qual Browser 4.3, and then MS/MS spectra were used to identify the chemical structures.
All data and images were analyzed unbiasedly. A random number was assigned to each group to ensure the investigator was blind to the pharmacological treatment grouping information. Statistical analysis was performed by using Graphpad Prism software 9.0, and T-test and one-way ANOVA were used for two- or multiple-group comparisons. p < 0.05 was considered statistically significant.
Huang R., Duan J., Huang W., Cheng Y., Zhu B, & Li F. (2024). Inhibition of CYP1A1 Alleviates Colchicine-Induced Hepatotoxicity. Toxins, 16(1), 35.
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5

Native Mass Spectrometry of Nucleosomes

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Nucleosomes samples at a concentration of 2 μM and desalted into 150 mM ammonium acetate using 30 kDa MWCO 0.5 mL spin filters (Millipore-Sigma). Samples were analyzed using a Q Exactive HF mass spectrometer with Extended Mass Range (QE-EMR) and a Q Exactive HF Ultra-High Mass Range (QE-UHMR), both by Thermo Fisher Scientific. Data were collected using XCalibur QualBrowser 4.0.27.10 (Thermo Fisher Scientific). The native electrospray platform is coupled to a three-tiered tandem MS process. First, the analysis of the intact nucleosome (MS1) provides the total complex mass (reported as a deconvoluted neutral average mass value).13 (link) In stage two, the nucleosome is activated by collisions with nitrogen gas to eject histones (MS2). In stage three, further vibrational activation of the ejected histones via collisions with nitrogen gas yields backbone fragmentation products from each monomer (MS3) that are recorded at isotopic resolution (120,000 resolving power at m/z 400). These fragments can be mapped onto the primary sequence of the histones in order to localize posttranslational modifications. A step-by-step protocol for Nuc-MS data acquisition and analysis is available on the Nature Protocol Exchange repository (DOI 10.21203/rs.3.pex-1288/v1) and in the Supplemental Information.34
Schachner L.F., Jooβ K., Morgan M.A., Piunti A., Meiners M.J., Kafader J.O., Lee A.S., Iwanaszko M., Cheek M.A., Burg J.M., Howard S.A., Keogh M.C., Shilatifard A, & Kelleher N.L. (2021). Decoding the Protein Composition of Whole Nucleosomes with Nuc-MS. Nature methods, 18(3), 303-308.
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6

Native Mass Spectrometry of Nucleosomes

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Nucleosomes samples at a concentration of 2 μM and desalted into 150 mM ammonium acetate using 30 kDa MWCO 0.5 mL spin filters (Millipore-Sigma). Samples were analyzed using a Q Exactive HF mass spectrometer with Extended Mass Range (QE-EMR) and a Q Exactive HF Ultra-High Mass Range (QE-UHMR), both by Thermo Fisher Scientific. Data were collected using XCalibur QualBrowser 4.0.27.10 (Thermo Fisher Scientific). The native electrospray platform is coupled to a three-tiered tandem MS process. First, the analysis of the intact nucleosome (MS1) provides the total complex mass (reported as a deconvoluted neutral average mass value).13 (link) In stage two, the nucleosome is activated by collisions with nitrogen gas to eject histones (MS2). In stage three, further vibrational activation of the ejected histones via collisions with nitrogen gas yields backbone fragmentation products from each monomer (MS3) that are recorded at isotopic resolution (120,000 resolving power at m/z 400). These fragments can be mapped onto the primary sequence of the histones in order to localize posttranslational modifications. A step-by-step protocol for Nuc-MS data acquisition and analysis is available on the Nature Protocol Exchange repository (DOI 10.21203/rs.3.pex-1288/v1) and in the Supplemental Information.34
Schachner L.F., Jooβ K., Morgan M.A., Piunti A., Meiners M.J., Kafader J.O., Lee A.S., Iwanaszko M., Cheek M.A., Burg J.M., Howard S.A., Keogh M.C., Shilatifard A, & Kelleher N.L. (2021). Decoding the Protein Composition of Whole Nucleosomes with Nuc-MS. Nature methods, 18(3), 303-308.
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7

Native Mass Spectrometry Characterization

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Protein samples were measured at a concentration of 2 μM and desalted into 150 mM ammonium acetate using 10–30 kDa MWCO 0.5 mL spin filters (Millipore-Sigma). Samples were analyzed using a Q Exactive HF mass spectrometer with Extended Mass Range (QE-EMR) by Thermo Fisher Scientific. Data were collected using XCalibur Qual Browser 4.0.27.10 (Thermo Fisher Scientific). The native electrospray platform was coupled to a three-tiered tandem MS process. First, the analysis of the intact complex (MS1) provides the total complex mass (reported as a deconvoluted neutral average mass value).21 (link) In stage two, the complex is activated by collisions with nitrogen gas to eject subunits (MS2). In stage three, further vibrational activation of the ejected subunits via collisions with nitrogen gas yields backbone fragmentation products from each monomer (MS3) that are recorded at isotopic resolution (120,000 resolving power at m/z 400). These fragments can be mapped onto the primary sequence of the subunits in order to localize PTMs.
Schachner L.F., Des Soye B., Ro S., Kenney G.E., Ives A.N., Su T., Goo Y.A., Jewett M.C., Rosenzweig A.C, & Kelleher N.L. (2022). Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation. ACS chemical biology, 17(10), 2769-2780.
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