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Related Concept Videos

Mass Spectrum01:23

Mass 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...
Mass Spectrometers01:16

Mass 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:
Mass Spectrum: Interpretation01:24

Mass 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...
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

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...
Mass Spectrometry: Overview01:19

Mass 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...
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...

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Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization (IR-MALDESI)
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Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization (IR-MALDESI)

Published on: March 24, 2016

Mass spectrometer output file format mzML.

Eric W Deutsch1

  • 1Institute for Systems Biology, Seattle, WA, USA, edeutsch@systemsbiology.org.

Methods in Molecular Biology (Clifton, N.J.)
|December 17, 2009
PubMed
Summary
This summary is machine-generated.

Mass spectrometry data sharing is improved with mzML, an open XML-based file format. This standard enables easier archiving, processing, and development of open-source software for biomolecular analysis.

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Area of Science:

  • Proteomics and Metabolomics
  • Biomolecular Analysis
  • Computational Biology

Background:

  • Mass spectrometry is crucial for analyzing biomolecular compounds.
  • Proprietary file formats from different vendors hinder data sharing and software development.
  • Lack of a standardized format limits interoperability in mass spectrometry data analysis.

Purpose of the Study:

  • To introduce mzML, an open XML-based format for mass spectrometry data.
  • To facilitate data archiving, sharing, and downstream analysis.
  • To promote the development of open-source software for mass spectrometry.

Main Methods:

  • Development of an XML schema defining the mzML file structure.
  • Creation of a controlled vocabulary for spectral metadata.
  • Implementation of semantic validation rules for ensuring data compliance.
  • Provision of comprehensive documentation and example files.

Main Results:

  • The mzML format provides a standardized structure for mass spectrometry data.
  • A controlled vocabulary ensures clear and consistent metadata definitions.
  • Semantic validation rules enhance data integrity and compliance.
  • Multiple software implementations and vendor support were available at release.

Conclusions:

  • The mzML format addresses the challenge of proprietary file formats in mass spectrometry.
  • It promotes data interoperability, sharing, and collaborative research.
  • The mzML standard is expected to accelerate innovation in open-source mass spectrometry software.