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Related Concept Videos

Weak Base Solutions03:21

Weak Base Solutions

25.4K
Some compounds produce hydroxide ions when dissolved by chemically reacting with water molecules. In all cases, these compounds react only partially and so are classified as weak bases. These types of compounds are also abundant in nature and important commodities in various technologies. For example, global production of the weak base ammonia is typically well over 100 metric tons annually, being widely used as an agricultural fertilizer, a raw material for chemical synthesis of other...
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Mass Spectrometry: Overview01:19

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Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electron ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave behind a...
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Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
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Mass Spectrometry of Amines01:15

Mass Spectrometry of Amines

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In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule; a molecule with an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight. Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit strong molecular ion peaks, but acyclic...
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Mass Spectrometry: Isotope Effect01:13

Mass Spectrometry: Isotope Effect

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Most elements exist in nature as a mixture of isotopes. The isotopes differ in weight due to their respective number of neutrons. The molecular weight of a molecule is different depending on the specific isotope of its elements involved. As a result, the mass spectrum of the molecule exhibits peaks from the same fragment at multiple positions. The positions of these mass signals depend on the mass differences between isotopes. Furthermore, the intensity of these signals is dependent on the...
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Strong Acid and Base Solutions03:22

Strong Acid and Base Solutions

36.0K
A strong acid is a compound that dissociates completely in an aqueous solution and produces a concentration of hydronium ions equal to the initial concentration of acid. For example, 0.20 M hydrobromic acid will dissociate completely in water and produces 0.20 M of hydronium ions and 0.20 M of bromide ions.
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Updated: Feb 11, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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XL-MSDigger: a deep learning-based, versatile solution for cross-linking mass spectrometry.

Moran Chen1,2,3, Yanhong Hao1, Xiao Huang1

  • 1The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, China.

Nature Communications
|February 9, 2026
PubMed
Summary
This summary is machine-generated.

A new deep learning platform, XL-MSDigger, enhances cross-linking mass spectrometry (XL-MS) data analysis. It improves protein structure and protein-protein interaction identification by accurately predicting cross-linked peptide properties.

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Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
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Area of Science:

  • Biochemistry
  • Proteomics
  • Computational Biology

Background:

  • Cross-linking mass spectrometry (XL-MS) is vital for studying protein structure and interactions.
  • Current XL-MS data processing and analysis methods have significant limitations, hindering in-depth analysis.

Purpose of the Study:

  • To develop a versatile deep learning-based platform, XL-MSDigger, to overcome XL-MS data analysis bottlenecks.
  • To enhance the accuracy and coverage of XL-MS identification and enable reliable false discovery rate evaluation.

Main Methods:

  • Built the XL-MSDigger platform centered on Deep4D-XL, a deep learning tool for predicting cross-linked peptide properties (retention time, collisional cross-section, fragment ion intensity).
  • Developed rescoring algorithms and workflows for both data-dependent acquisition (DDA) and data-independent acquisition (DIA) analysis.
  • Enabled DIA-based XL-MS analysis using predicted spectral libraries.

Main Results:

  • Improved coverage of DDA-based XL-MS identification.
  • Achieved false discovery rate evaluation and high-reliability identification for DIA-based XL-MS analysis.
  • Enhanced detection of protein-protein interactions using DIA-based XL-MS with predicted spectral libraries.

Conclusions:

  • XL-MSDigger provides a general solution to significantly enhance XL-MS analysis performance.
  • The platform addresses key limitations in XL-MS data processing, paving the way for more comprehensive structural and interaction studies.
  • Deep learning-based prediction of peptide properties is effective in improving XL-MS data interpretation.