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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 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...
Mass Analyzers: Overview01:13

Mass Analyzers: Overview

The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
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: 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...

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Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
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Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

jmzML, an open-source Java API for mzML, the PSI standard for MS data.

Richard G Côté1, Florian Reisinger, Lennart Martens

  • 1EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.

Proteomics
|February 4, 2010
PubMed
Summary
This summary is machine-generated.

jmzML is a Java API for processing large mzML files efficiently. It uses advanced XML parsing for minimal memory usage and on-the-fly reference resolution, simplifying proteomics data analysis.

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Last Updated: Jun 16, 2026

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
09:29

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Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models
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Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization (IR-MALDESI)
10:47

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

Published on: March 24, 2016

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • The Proteomics Standards Initiative (PSI) mzML format is crucial for standardizing mass spectrometry data.
  • Handling large mzML files efficiently presents a significant challenge in proteomics data analysis.
  • Existing tools may require substantial memory or lack efficient methods for accessing data within large files.

Purpose of the Study:

  • To develop a Java API (jmzML) for the mzML data standard.
  • To enable efficient and memory-minimal processing of large mzML files.
  • To provide seamless handling of internal XML references within mzML data.

Main Methods:

  • Leveraging the Java Architecture for XML Binding (JAXB).
  • Implementing an XPath-based XML indexer for random-access parsing.
  • Developing on-the-fly resolution for internal XML references.

Main Results:

  • jmzML allows processing of arbitrarily large mzML files with minimal memory footprint.
  • The library facilitates easy and efficient manipulation of mzML data using Java.
  • Internal XML references are automatically resolved during processing.

Conclusions:

  • jmzML offers a robust and efficient solution for programmatic access to mzML data.
  • The API simplifies the development of proteomics software that utilizes mzML files.
  • The availability of jmzML, including a viewer, promotes wider adoption and data analysis in proteomics.