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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...
Matrix-Assisted Laser Desorption Ionization (MALDI)01:08

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...
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.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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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Related Experiment Video

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Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer
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Published on: November 26, 2013

A new method for alignment of LC-MALDI-TOF data.

Zhiqun Tang1, Lihua Zhang, Amrita K Cheema

  • 1Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA. hwr@georgetown.edu.

Proteome Science
|December 15, 2011
PubMed
Summary

This study introduces a novel alignment strategy for liquid chromatography-matrix assisted laser desorption/ionization time-of-flight (LC-MALDI-TOF) data. Incorporating intensity measurements alongside retention time and mass-to-charge ratio improves the accuracy of label-free differential protein expression analysis.

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Characterization of Synthetic Polymers via Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) Mass Spectrometry
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Last Updated: May 26, 2026

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer
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Published on: November 26, 2013

Characterization of Synthetic Polymers via Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) Mass Spectrometry
06:56

Characterization of Synthetic Polymers via Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) Mass Spectrometry

Published on: June 10, 2018

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biotechnology

Background:

  • Liquid chromatography coupled to mass spectrometry (LC-MS) is vital for label-free differential protein expression studies.
  • Variations in mass-to-charge ratio (m/z) and retention time (RT) necessitate data alignment across multiple runs.
  • Accurate alignment is crucial for comparing peptides and proteins in complex mixtures.

Purpose of the Study:

  • To develop an improved alignment strategy for LC-MALDI-TOF data.
  • To enhance the accuracy of label-free differential proteomics by addressing m/z and RT variations.
  • To leverage three-dimensional data (RT, m/z, intensity) for more robust alignment.

Main Methods:

  • Proposed a novel alignment strategy combining quality threshold cluster analysis and support vector regression.
  • Developed a method for aligning LC-MALDI-TOF data using three dimensions: RT, m/z, and intensity.
  • Utilized spike-in datasets for method validation and comparison.

Main Results:

  • Demonstrated the effectiveness of the proposed alignment method on both published and in-house generated spike-in datasets.
  • Showcased enhanced alignment performance compared to methods using only RT and m/z dimensions.
  • Confirmed that incorporating intensity measurements significantly improves alignment accuracy.

Conclusions:

  • The proposed three-dimensional alignment strategy is suitable for LC-MALDI-TOF data.
  • The inclusion of intensity data provides superior alignment performance in label-free proteomics.
  • This method offers a more reliable approach for differential protein expression analysis.