Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

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 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 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...
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 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 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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The Potential of Digital Twins for Pediatric Rare Diseases.

CPT: pharmacometrics & systems pharmacology·2026
Same author

From FAIR to CURE: guidelines for computational models of biological systems.

NPJ systems biology and applications·2026
Same author

The 2025 Westlake Autumn Symposium for Al Proteomics and Virtual Cell.

Genomics, proteomics & bioinformatics·2026
Same author

ACVI-Med, an open source variant interpretation tool for medical genomics.

BMC bioinformatics·2026
Same author

Indolent primary cutaneous B-cell lymphomas resemble persistent antigen reactions without signs of dedifferentiation.

Nature communications·2026
Same author

Kupffer Cell-Derived Tnf Triggers Cholangiocellular Tumorigenesis through JNK due to Chronic Mitochondrial Dysfunction and ROS.

Cancer cell·2026
Same journal

Light-Induced Proteomic Changes in Pseudomonas aeruginosa Biofilms.

Proteomics·2026
Same journal

Decade-Resolved Proteomic Profiling of Gastric Cancer FFPE Archives: Evaluating Storage-Associated Shifts and Signal Stability Over 50 Years.

Proteomics·2026
Same journal

Proteome-Scale Mining of Metal-Associated Proteins of Monkeypox Virus.

Proteomics·2026
Same journal

Optimized Sample Handling Minimizes Peptide Adsorption to Plastics to Enable High Sensitivity Evosep Based Chemical Proteomics.

Proteomics·2026
Same journal

Toward Predicting Pandemic Potential: A Comparative Analysis of Virus-Host Interactions Between Diverse Influenza A Viruses and the Human Innate Immune System.

Proteomics·2026
Same journal

Functional Divergence of Mucus in Pacific Oyster (Crassostrea gigas): Insights From Integrated Proteomic and Rheological Study.

Proteomics·2026
See all related articles

Related Experiment Video

Updated: May 22, 2026

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models
08:14

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models

Published on: December 5, 2014

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Johannes Griss1, Florian Reisinger, Henning Hermjakob

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

Proteomics
|April 28, 2012
PubMed
Summary
This summary is machine-generated.

The jmzReader library simplifies mass spectrometry (MS) data analysis by providing Java APIs to parse common MS formats. It streamlines software development for mzIdentML by offering a unified interface for external spectra data.

More Related Videos

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics
13:02

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Published on: October 5, 2016

Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues
06:43

Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues

Published on: June 21, 2018

Related Experiment Videos

Last Updated: May 22, 2026

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models
08:14

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models

Published on: December 5, 2014

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics
13:02

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Published on: October 5, 2016

Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues
06:43

Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues

Published on: June 21, 2018

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Proteomics

Background:

  • Mass spectrometry (MS) data is crucial for proteomics research.
  • Various data formats (DTA, MS2, MGF, PKL, mzXML, mzData, mzML) exist, complicating data integration.
  • The mzIdentML standard facilitates reporting peptide and protein identifications but does not contain spectra data.

Purpose of the Study:

  • To introduce the jmzReader library, a Java API for parsing common mass spectrometry data formats.
  • To facilitate the use of mzIdentML by providing a unified interface for accessing external spectral data.
  • To simplify the development of software that utilizes mzIdentML and associated spectral data.

Main Methods:

  • Development of a Java library (jmzReader) offering APIs to parse DTA, MS2, MGF, PKL, mzXML, mzData, and mzML formats.
  • Implementation of a common interface within jmzReader to handle spectral data references used by mzIdentML.
  • Integration of existing jmzML API for mzML parsing.

Main Results:

  • The jmzReader library successfully parses multiple common mass spectrometry data formats.
  • A unified interface is provided, simplifying the process for developers working with mzIdentML.
  • The library reduces the need for developers to support multiple individual MS data file formats.

Conclusions:

  • jmzReader enhances the usability of the mzIdentML standard by simplifying access to external spectral data.
  • The library offers a significant advantage for software development in proteomics, reducing complexity and improving efficiency.
  • The open-source jmzReader library, including a viewer and documentation, is available for download.