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Related Concept Videos

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...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
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:

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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MSQuant, an open source platform for mass spectrometry-based quantitative proteomics.

Peter Mortensen1, Joost W Gouw, Jesper V Olsen

  • 1Department of Biochemistry and Molecular Biology, University of Southern Denmark, Center for Experimental Bioinformatics, Odense, Campusvej 55, DK-5230 Odense M, Denmark.

Journal of Proteome Research
|November 6, 2009
PubMed
Summary
This summary is machine-generated.

MSQuant is an open-source software for mass spectrometry proteomics. It enhances peptide identification accuracy and supports various quantitation methods, accelerating research by overcoming software limitations.

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Area of Science:

  • Proteomics
  • Computational Biology
  • Biochemistry

Background:

  • Mass spectrometry-based proteomics relies heavily on data interpretation algorithms.
  • Proprietary software solutions limit the rapid advancement of proteomics technology due to their closed nature and slow development cycles.

Purpose of the Study:

  • To develop an open-source software environment, MSQuant, for visualizing and validating peptide identification results directly from raw mass spectrometric data.
  • To improve the accuracy and reduce false positives in peptide identifications and enable robust protein quantitation.

Main Methods:

  • Developed MSQuant, an open-source software environment for mass spectrometry data analysis.
  • Implemented iterative recalibration of mass spectrometry data to enhance mass accuracy.
  • Integrated algorithms including an MS(3) score for peptide identification and a post-translational modification (PTM) score for residue-specific modification probability.

Main Results:

  • MSQuant significantly increases mass accuracy, leading to a reduction in false positive peptide identifications.
  • The software provides tools for validating peptide identifications against raw mass spectrometry data.
  • MSQuant supports various relative protein quantitation strategies, including label-based (e.g., SILAC, ICAT, mTRAQ, (15)N, (18)O) and label-free approaches.

Conclusions:

  • MSQuant offers an open-source solution to overcome limitations of vendor-supplied software in proteomics.
  • The software enhances data quality and accuracy for peptide identification and protein quantitation.
  • MSQuant is available for download, facilitating broader adoption and development in the proteomics community.