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Related Concept Videos

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...
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 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...

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Related Experiment Video

Updated: May 11, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Methods and algorithms for quantitative proteomics by mass spectrometry.

Rune Matthiesen1, Ana Sofia Carvalho

  • 1Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.

Methods in Molecular Biology (Clifton, N.J.)
|May 14, 2013
PubMed
Summary
This summary is machine-generated.

This study overviews common mass spectrometry (MS) methods and algorithms for quantitative proteomics. It provides computational strategies for reliable protein and peptide quantitation, enabling flexible data analysis across diverse experimental setups.

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Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Mass spectrometry (MS) offers combined protein identification and quantitation, unlike protein arrays.
  • Numerous quantitative MS methods exist for proteins and peptides.
  • Data analysis often requires integrating multiple software solutions.

Purpose of the Study:

  • To overview common MS methods and algorithms in quantitative proteomics.
  • To discuss computational algorithms for reliable protein, peptide, and posttranslational modification quantitation.
  • To provide implementable algorithms and resources for data analysis.

Main Methods:

  • Review of common mass spectrometry techniques for quantitation.
  • Discussion of computational algorithms for peptide and protein quantification.
  • Exploration of strategies for analyzing posttranslational modifications.

Main Results:

  • Identified common quantitative mass spectrometry methods and algorithms.
  • Detailed computational approaches for reliable protein and peptide quantitation.
  • Provided resources and algorithmic ideas for scripting languages like R and Python.

Conclusions:

  • Understanding algorithmic principles allows flexible analysis of diverse proteomic data.
  • The presented strategies offer a valuable alternative to "black box" analysis tools.
  • Enables reliable quantitation of proteins, peptides, and PTMs independent of instrument or protocol.