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Related Concept Videos

MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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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 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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Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

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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...
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Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
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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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Related Experiment Video

Updated: Apr 1, 2026

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

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Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery.

H López-Fernández1,2, H M Santos3, J L Capelo4

  • 1Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. hlfernandez@uvigo.es.

BMC Bioinformatics
|October 7, 2015
PubMed
Summary

Mass-Up is a new, free software application designed for researchers using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). It simplifies knowledge discovery from complex proteomic data without requiring programming skills.

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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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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

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Bioinformatics

Background:

  • Mass spectrometry is crucial in proteomics, with MALDI-TOF-MS widely used for protein and peptide analysis due to its speed and sensitivity.
  • Integrating Machine Learning and statistical methods with MALDI-TOF-MS enables advanced knowledge discovery.
  • Existing software solutions often require programming skills, highlighting a need for user-friendly, integrated tools.

Purpose of the Study:

  • To present Mass-Up, an open-source, multiplatform application for knowledge discovery from MALDI-TOF-MS data.
  • To provide researchers with an all-in-one graphical user interface solution.
  • To eliminate the need for programming expertise in MALDI-TOF-MS data analysis.

Main Methods:

  • Development of Mass-Up, an open-source software application.
  • Implementation of data preprocessing functionalities.
  • Integration of various analytical methods including biomarker discovery, clustering, biclustering, PCA visualization, and classification.

Main Results:

  • Mass-Up offers a comprehensive suite of tools for MALDI-TOF-MS data analysis.
  • The software supports biomarker discovery, clustering, biclustering, and classification of spectral data.
  • It includes a three-dimensional Principal Component Analysis (PCA) visualization feature for enhanced data exploration.

Conclusions:

  • Mass-Up democratizes knowledge discovery for MALDI-TOF-MS researchers by providing an accessible, integrated platform.
  • The software is open-source, free, and distributed under the GPLv3 license.
  • Mass-Up is available at http://sing.ei.uvigo.es/mass-up.