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Related Concept Videos

MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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...
High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For example, the mass of helium...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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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Matrix-Assisted Laser Desorption Ionization (MALDI)

Matrix-assisted laser desorption ionization (MALDI) is a powerful analytical technique used in mass spectrometry. It enables the identification and characterization of various biomolecules, including proteins, peptides, nucleic acids, and carbohydrates. MALDI is an ionization technique, widely employed in biological and medical research, as well as in fields like pharmacology and biochemistry.The analyte of interest, a biomolecule or a mixture of biomolecules, is mixed with a suitable matrix...

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Related Experiment Video

Updated: Jul 10, 2026

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer
09:38

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Published on: November 26, 2013

Persistent Homology as a Detection Axis Complementary to Intensity-Based Methods for Comparative MALDI Mass

Shinichi Yamaguchi1, Yuzuki Morita2, Hiromichi Suetani3,4

  • 1Shimadzu Corporation, Kyoto 604-8511, Japan.

Journal of the American Society for Mass Spectrometry
|July 8, 2026
PubMed
Summary

Persistent homology (PH) offers a novel, alignment-free method to compare spatial molecular distributions in mass spectrometry imaging (MSI) data. This approach reveals molecular patterns missed by traditional intensity-based methods, identifying potential biomarkers in lung lipidomics.

Keywords:
MALDIcomplementary methodscoregistration-freelipidomicslungmass spectrometry imagingpersistent homologytopological data analysis

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Sample Preparation for Metabolic Profiling using MALDI Mass Spectrometry Imaging
09:08

Sample Preparation for Metabolic Profiling using MALDI Mass Spectrometry Imaging

Published on: December 22, 2020

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Last Updated: Jul 10, 2026

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer
09:38

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Published on: November 26, 2013

Sample Preparation for Metabolic Profiling using MALDI Mass Spectrometry Imaging
09:08

Sample Preparation for Metabolic Profiling using MALDI Mass Spectrometry Imaging

Published on: December 22, 2020

Area of Science:

  • Computational Biology
  • Mass Spectrometry Imaging (MSI)
  • Bioinformatics

Background:

  • Comparing spatial molecular distributions in MSI is challenging due to variations in section shape and intensity.
  • Intensity-based methods often overlook crucial spatial organization patterns.
  • Existing techniques lack alignment-free frameworks for robust dissimilarity quantification.

Purpose of the Study:

  • To introduce and validate a novel alignment-free framework using persistent homology (PH) for spatial dissimilarity analysis in MSI.
  • To compare PH-based candidate identification with traditional intensity-based methods (Kolmogorov-Smirnov, Earth Mover's Distance).
  • To assess the utility of PH in identifying sex-specific molecular patterns in lung lipidomics data.

Main Methods:

  • Applied persistent homology (PH) with z-score normalization and 1-Wasserstein (W1) distance to MALDI-MSI lung lipidomics data.
  • Screened 1000 m/z channels across 15 pairwise comparisons, prioritizing directional consistency.
  • Compared PH results with Kolmogorov-Smirnov (KS) and Earth Mover's Distance (EMD) baselines and control analyses.

Main Results:

  • The PH framework identified 16 candidates in the female cohort (8 with strong spatial support) and 1 in the male cohort.
  • PH identified distinct molecular patterns compared to KS and EMD, with minimal overlap at primary parameters.
  • PH acts as a complementary detection axis, partially orthogonal to intensity-based screening, highlighting candidates for further MS/MS identification.

Conclusions:

  • Persistent homology provides a powerful, alignment-free method for quantifying spatial dissimilarity in MSI data.
  • This topological approach effectively identifies potential molecular biomarkers missed by conventional intensity-based analyses.
  • The PH framework is valuable for discovering sex-specific spatial lipidomic patterns and prioritizing targets for targeted mass spectrometry validation.