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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.
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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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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Introduction to Mass Spectrometry-Based Proteomics.

Rune Matthiesen1, Jakob Bunkenborg2

  • 1Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal. runem2009@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|September 26, 2019
PubMed
Summary
This summary is machine-generated.

Mass spectrometry (MS) is vital for protein identification and quantification in proteomics. This chapter outlines MS-based proteomics concepts, analytical choices, and data processing for comprehensive proteome exploration.

Keywords:
Data formatsMass spectrometryProteomicsSample preparation

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Area of Science:

  • Proteomics
  • Analytical Chemistry

Background:

  • Mass spectrometry (MS) is a key technology for determining the mass of ionized molecules.
  • Its application in proteomics enables global protein identification and quantification.
  • Various applications necessitate careful consideration of analytical choices and instrumental limitations.

Purpose of the Study:

  • To provide an overview of mass spectrometry-based proteomics.
  • To discuss essential concepts, analytical choices, and data processing steps.
  • To guide researchers in selecting appropriate MS setups for proteomic studies.

Main Methods:

  • Review of mass spectrometry principles and instrumentation.
  • Discussion of sample preparation techniques relevant to proteomics.
  • Overview of data processing strategies for MS-based proteomics.

Main Results:

  • Highlights the multifaceted nature of handling mass spectrometry data.
  • Emphasizes the importance of user decisions in obtaining comprehensive proteomic information.
  • Introduces commonly used MS setups and key concepts in the field.

Conclusions:

  • Effective utilization of MS in proteomics requires informed decisions on sample preparation, instrumentation, and data analysis.
  • Understanding these factors is crucial for exploring different aspects of the proteome.
  • This chapter serves as a foundational guide for advanced topics in MS-based proteomics.