Related Experiment Video
Updated: Aug 3, 2026
10:47
Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization (IR-MALDESI)
Published on: March 24, 2016
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
Mikko Katajamaa1, Jarkko Miettinen, Matej Oresic
1Turku Centre for Biotechnology Turku, Finland.
Bioinformatics (Oxford, England)
|January 13, 2006
Summary
New methods enhance mass spectrometry data analysis within MZmine software. These tools improve processing, visualization, and exploratory analysis for molecular profiles.
Area of Science:
- Computational chemistry
- Bioinformatics
- Analytical chemistry
Background:
- Mass spectrometry is a powerful technique for molecular profiling.
- Efficient data processing and visualization are crucial for interpreting complex mass spectrometry datasets.
- The MZmine software provides a platform for mass spectrometry data analysis.
Purpose of the Study:
- To introduce new methods for processing and visualizing mass spectrometry-based molecular profile data.
- To extend the capabilities of the MZmine software.
- To facilitate exploratory data analysis and improve the interpretation of molecular profiles.
Main Methods:
- Implementation of new features and extensions within the MZmine software.
- Support for mzXML data format.
- Batch and parallel processing capabilities for handling large datasets.
- Novel peak area calculation methods using post-alignment peak picking.
- Integration of Sammon's mapping and curvilinear distance analysis for data visualization.
Main Results:
- Enhanced processing capabilities for mass spectrometry data.
- Improved visualization techniques for molecular profiles.
- Increased efficiency in handling and analyzing large-scale datasets.
- Advanced tools for exploratory data analysis.
Conclusions:
- The new methods significantly improve the processing and visualization of mass spectrometry data.
- The extended MZmine software offers a more comprehensive solution for molecular profile analysis.
- These advancements aid in the interpretation and discovery of molecular features.
Related Concept Videos
01:19Mass Spectrometry: Overview
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...
01:23Mass Spectrum
A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...
01:16Mass Spectrometers
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:
01:19MALDI-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...
01:24Mass Spectrum: Interpretation
An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
01:21Tandem 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...