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Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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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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Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

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The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
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Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
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Mass Spectrometers01:16

Mass Spectrometers

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This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:
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MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
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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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Updated: Feb 21, 2026

Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports
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Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry.

Joe Wandy1, Yunfeng Zhu2, Justin J J van der Hooft1

  • 1Glasgow Polyomics University of Glasgow, Glasgow, UK.

Bioinformatics (Oxford, England)
|October 3, 2017
PubMed
Summary
This summary is machine-generated.

MS2LDA is a new method for analyzing metabolomics data. The ms2lda.org web application makes this powerful tool accessible for researchers to explore molecular fragment data and identify Mass2Motifs.

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Area of Science:

  • Computational Biology
  • Metabolomics
  • Bioinformatics

Background:

  • Metabolomics experiments generate large sets of molecular fragment data.
  • MS2LDA is a previously published method for decomposing this data.
  • A user-friendly web application is needed to increase accessibility.

Purpose of the Study:

  • To present ms2lda.org, a web application for the MS2LDA method.
  • To enable researchers to upload data, perform analyses, and visualize results.
  • To facilitate the decomposition of molecular fragment data.

Main Methods:

  • The ms2lda.org web application accepts tandem mass spectrometry data in standard formats.
  • Users can infer co-occurring fragment and neutral loss features (Mass2Motifs).
  • An alternative workflow allows decomposition onto predefined Mass2Motifs via web interface or web service.

Main Results:

  • The web application provides interactive visualizations for exploring analysis results.
  • Users can identify sets of fragment and neutral loss features (Mass2Motifs).
  • Both de novo Mass2Motif inference and decomposition onto existing motifs are supported.

Conclusions:

  • ms2lda.org enhances the accessibility of the MS2LDA method for the research community.
  • The platform supports data upload, analysis, and result exploration.
  • The tool can be accessed via a web interface or programmatically.