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Related Concept Videos

2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)01:19

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Heteronuclear single-quantum correlation spectroscopy (HSQC) is a 2D NMR technique that reveals one-bond correlations between hydrogen and a heteronucleus. The HSQC experiment is similar to the heteronuclear correlation experiment (HETCOR) but is more sensitive. In the HSQC spectrum, the proton chemical shift is plotted on the horizontal F2 axis, while the 13C chemical shift is plotted on the vertical F1 axis. The corresponding proton and 13C spectra are also shown. The HSQC contour plot does...
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The single-compartment model serves as a simplified representation of the human body. This model assumes that the body functions as a single, well-mixed open compartment. When a drug is administered intravenously, it enters the body and quickly distributes uniformly. The drug then undergoes biotransformation and elimination, ultimately leaving the body. The volume of this compartment is referred to as the apparent volume of distribution into which the drug can uniformly distribute. In this...
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Compartment Models: Two-Compartment Model01:20

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The two-compartment model divides the body into central and peripheral compartments to account for varying blood perfusion rates among organs and tissues, affecting drug distribution. The central compartment includes blood and highly perfused tissues with rapid drug distribution, while the peripheral compartment contains tissues with slower drug distribution. After a single IV bolus dose, the drug concentration is high in plasma and low in tissues. The drug distribution between compartments...
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Chemical Shift: Internal References and Solvent Effects01:17

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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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¹H NMR of Labile Protons: Temporal Resolution01:10

¹H NMR of Labile Protons: Temporal Resolution

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Protons bonded to heteroatoms such as nitrogen and oxygen exhibit a range of chemical shift values. This is due to the varying degree of hydrogen bonding between the proton and the heteroatom in other molecules. The extent of hydrogen bonding affects the electron density around the proton, thereby giving different chemical shift values for the protons in the proton NMR spectrum.
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Inductive Effects on Chemical Shift: Overview01:27

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The protons in unsubstituted alkanes are strongly shielded with chemical shifts below 1.8 ppm. Methine, methylene, and methyl protons appear at approximately 1.7, 1.2 and 0.7 ppm, while the proton signal from methane appears at 0.23 ppm. An electronegative substituent, such as chlorine, withdraws the electron density from the protons, increasing their chemical shift. Progressive substitution of the hydrogens in methane by chlorine shifts the proton signals increasingly downfield, to 3.05 ppm in...
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Related Experiment Video

Updated: May 26, 2025

Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging cPILOT
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Isobaric Labeling Update in MaxQuant.

Daniela Ferretti1, Pelagia Kyriakidou1, Jinqiu Xiao1

  • 1Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.

Journal of Proteome Research
|February 25, 2025
PubMed
Summary
This summary is machine-generated.

MaxQuant software now improves isobaric labeling analysis with impurity correction and weighted median normalization. This update enhances accuracy and reduces batch effects in complex proteomic datasets, including single-cell and phosphorylation studies.

Keywords:
FAIMSMaxQuantTMTUMAPbatch effectshuman body mapisobaric labelingnormalizationsingle cell proteomicst-SNEweighted median normalization

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Area of Science:

  • Proteomics and Mass Spectrometry
  • Computational Biology and Bioinformatics

Background:

  • Isobaric labeling techniques like TMT Pro are crucial for quantitative proteomics.
  • Accurate analysis of complex proteomic data requires robust software tools.
  • Challenges include reporter ion impurities and batch effects in large-scale studies.

Purpose of the Study:

  • To present an updated version of the MaxQuant software for isobaric labeling data analysis.
  • To evaluate the performance of new features using benchmark datasets.
  • To improve the accuracy and reduce systematic errors in quantitative proteomics.

Main Methods:

  • Implementation of impurity correction factors for isobaric labels (e.g., TMT Pro).
  • Direct analysis of TMT data combined with FAIMS separation.
  • Application of weighted median normalization to diverse datasets, including human body atlas data.

Main Results:

  • Impurity correction significantly improves accuracy, demonstrated on a single-cell multispecies mixture.
  • Weighted median normalization effectively removes or reduces batch effects, leading to biologically meaningful clustering.
  • Normalization performs well even without using reference channels, simplifying experimental design.

Conclusions:

  • The updated MaxQuant software offers enhanced capabilities for analyzing isobaric labeling data.
  • New features improve data accuracy, reduce batch effects, and simplify analysis workflows.
  • MaxQuant provides a powerful, freely available tool for quantitative proteomics research.