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Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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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...
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MALDI-TOF Mass Spectrometry01:19

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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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Mass Spectrometers01:16

Mass Spectrometers

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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:
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Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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...
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Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

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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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Mass Spectrum01:23

Mass Spectrum

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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...
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MzJava: An open source library for mass spectrometry data processing.

Oliver Horlacher1, Frederic Nikitin2, Davide Alocci1

  • 1Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva 1211, Switzerland; Centre Universitaire de Bioinformatique, University of Geneva, Geneva 1211, Switzerland.

Journal of Proteomics
|July 5, 2015
PubMed
Summary
This summary is machine-generated.

MzJava is an open-source Java API simplifying mass spectrometry data analysis. It offers tools for processing spectra and biological molecules, enhancing code sharing for bioinformaticians.

Keywords:
GlycomicsHadoopJavaMass spectrometryProteomicsSpark

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Analytical Chemistry

Background:

  • Mass spectrometry (MS) is crucial for high-throughput molecular identification in biological samples.
  • Sharing and reusing code for MS data analysis presents challenges for bioinformaticians.

Purpose of the Study:

  • To develop MzJava, an open-source Java Application Programming Interface (API) for efficient mass spectrometry data processing.
  • To provide robust data structures and algorithms for analyzing spectra and associated biological molecules.

Main Methods:

  • Implementation of data structures and algorithms for mass spectra and biological molecules (metabolites, glycans, peptides).
  • Inclusion of functionalities for mass calculation, peak processing, spectrum alignment, clustering, protein digestion, and fragmentation.
  • Development of scoring functions for spectrum-spectrum and peptide/glycan-spectrum matching.
  • Integration of readers/writers for common data formats and support for Hadoop MapReduce and Apache Spark.

Main Results:

  • MzJava offers comprehensive tools for MS data processing, including advanced analytical functions.
  • The API supports cluster computing frameworks, enabling scalable analysis.
  • Adherence to software engineering best practices ensures code correctness and usability.

Conclusions:

  • MzJava provides a valuable, open-source resource for the computational proteomics and metabolomics communities.
  • The library facilitates reproducible and efficient analysis of mass spectrometry data.
  • Its design promotes code sharing and reuse among researchers working with MS data.