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Related Concept Videos

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 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...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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...
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:
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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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Updated: May 31, 2026

A Strategy for Sensitive, Large Scale Quantitative Metabolomics
14:18

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

Published on: May 27, 2014

MassChroQ: a versatile tool for mass spectrometry quantification.

Benoît Valot1, Olivier Langella, Edlira Nano

  • 1INRA, PAPPSO, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, UMR0320 de Génétique Végétale, Gif sur Yvette, France. valot@moulon.inra.fr

Proteomics
|July 14, 2011
PubMed
Summary
This summary is machine-generated.

MassChroQ is a versatile software for liquid chromatography-mass spectrometry (LC-MS) data analysis. It offers accurate peptide quantification across various labeling strategies and mass spectrometry systems, improving reproducibility.

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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An HS-MRM Assay for the Quantification of Host-cell Proteins in Protein Biopharmaceuticals by Liquid Chromatography Ion Mobility QTOF Mass Spectrometry
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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

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Bioinformatics

Background:

  • Numerous software tools exist for LC-MS quantification, but often lack versatility.
  • Existing tools are frequently limited to specific quantification strategies (label-free, isotopic labeling) or mass spectrometry systems (high/low resolution).

Purpose of the Study:

  • To develop a versatile software tool, MassChroQ (Mass Chromatogram Quantification), for robust LC-MS data alignment and peptide quantification.
  • To provide a flexible solution applicable to diverse experimental setups, including various labeling techniques and mass spectrometry resolutions.

Main Methods:

  • MassChroQ performs data alignment and peptide quantification via peak area integration on extracted ion chromatograms.
  • It supports automatic or manual peptide selection (m/z and retention time) and handles large-scale experiments with fractionation (e.g., SDS-PAGE, 2D LC).

Main Results:

  • Evaluations on complex label-free LC-MS data demonstrated high technical reproducibility with low coefficients of variation (1.4%).
  • The software achieved high correlation coefficients (0.98) with protein quantity, indicating accurate quantification.
  • MassChroQ is fully configurable, ensures traceability, uses open data formats, and integrates into existing proteomic pipelines.

Conclusions:

  • MassChroQ offers a versatile, accurate, and reproducible solution for peptide quantification in LC-MS analyses.
  • Its adaptability to different labeling strategies and mass spectrometry systems makes it a valuable tool for the proteomics community.
  • The software is freely available, promoting accessibility and integration into standard bioinformatics workflows.