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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...
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...
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...
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High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For example, the mass of helium...
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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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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
09:35

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Protein identification using MS/MS data.

John S Cottrell1

  • 1Matrix Science Ltd., London, UK. jcottrell@matrixscience.com

Journal of Proteomics
|June 4, 2011
PubMed
Summary
This summary is machine-generated.

This tutorial focuses on protein identification using tandem mass spectrometry (MS/MS) data. It covers practical database searching techniques for accurate protein characterization and modification analysis.

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Last Updated: Jun 1, 2026

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Area of Science:

  • Proteomics
  • Biochemistry
  • Mass Spectrometry

Background:

  • Mass spectrometry-based proteomics is crucial for identifying and characterizing proteins.
  • Database searching of MS/MS data is a primary method for protein identification.
  • Understanding practical aspects enhances the reliability of proteomic analyses.

Purpose of the Study:

  • To provide an introductory tutorial on protein identification and characterization using MS/MS database searching.
  • To emphasize practical considerations in database searching, including database selection and mass tolerance.
  • To discuss the identification of post-translational modifications and inferring protein presence from peptide data.

Main Methods:

  • Database searching of tandem mass spectrometry (MS/MS) data.
  • Evaluation of sequence database choices and mass tolerance parameters.
  • Methods for identifying post-translational modifications.

Main Results:

  • Discussion on the trade-offs between sensitivity and specificity in protein identification.
  • Exploration of challenges in inferring protein abundance from peptide match data.
  • Practical guidance on optimizing database search parameters.

Conclusions:

  • Effective protein identification relies on careful selection of databases and search parameters.
  • Understanding post-translational modifications is key to comprehensive protein characterization.
  • This tutorial provides foundational knowledge for MS/MS data analysis in proteomics.