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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 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: 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...
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...

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

pymzML--Python module for high-throughput bioinformatics on mass spectrometry data.

Till Bald1, Johannes Barth, Anna Niehues

  • 1Institute of Plant Biology and Biotechnology, University of Muenster, 48143 Muenster, Germany.

Bioinformatics (Oxford, England)
|February 4, 2012
PubMed
Summary
This summary is machine-generated.

pymzML provides easy access to mass spectrometry (MS) data, featuring a fast mzML parser and spectral handling functions for rapid tool development in Python.

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Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
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Last Updated: May 25, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
10:05

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Published on: October 24, 2018

Area of Science:

  • Computational chemistry
  • Bioinformatics
  • Data science

Background:

  • Mass spectrometry (MS) data analysis requires efficient tools.
  • The mzML format is the standard for MS data.
  • Developing custom MS data analysis tools can be challenging.

Purpose of the Study:

  • To introduce pymzML, a Python extension for MS data.
  • To facilitate the development of new MS data analysis tools.
  • To provide efficient handling of mzML files.

Main Methods:

  • pymzML is a Python module compatible with Python 2.6.5+ and Python 3.
  • It offers direct access to mass spectrometry data.
  • Includes a fast parser for mzML files and functions for spectral manipulation.

Main Results:

  • pymzML enables easy access to mass spectrometry data.
  • It provides a very fast parser for the mzML standard format.
  • Offers a suite of functions for comparing and handling spectra.

Conclusions:

  • pymzML simplifies and accelerates the development of MS data analysis tools.
  • Its efficient parsing and spectral handling capabilities are key benefits.
  • The module enhances accessibility and usability of mass spectrometry data.