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Related Concept Videos

Proteomics01:33

Proteomics

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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...
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Peptide Identification Using Tandem Mass Spectrometry01:33

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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.
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...
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Software Options for the Analysis of MS-Proteomic Data.

Avinash Yadav1, Federica Marini1, Alessandro Cuomo1

  • 1Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy.

Methods in Molecular Biology (Clifton, N.J.)
|July 8, 2021
PubMed
Summary

Mass spectrometry (MS)-based proteomics is a key method for analyzing biological samples. This chapter details bioinformatics tools for processing complex shotgun proteomics data, aiding protein identification and quantification.

Keywords:
AlgorithmsDatabasesMass spectrometryProtein identificationProtein quantificationShotgun proteomicsSoftware

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Analytical Chemistry

Background:

  • Mass spectrometry (MS)-based proteomics is a leading technique for analyzing peptides and proteins in biological samples.
  • High-resolution mass spectrometers generate substantial data, particularly in shotgun/bottom-up proteomics.
  • Shotgun proteomics involves enzymatic digestion of proteins into peptides for MS analysis using data-dependent acquisition (DDA).

Purpose of the Study:

  • To present popular bioinformatics solutions for analyzing shotgun MS-proteomics data.
  • To provide an overview of data preprocessing options and available search engines.
  • To offer practical guidance on optimizing parameters for peptide search in MS-proteomics.

Main Methods:

  • Review of established bioinformatics tools and platforms for MS-proteomics data analysis.
  • Description of data preprocessing techniques relevant to shotgun proteomics.
  • Explanation of various search engine functionalities and parameter optimization strategies.

Main Results:

  • Identification of widely used bioinformatics solutions for large-scale protein identification and quantification.
  • Discussion of essential data preprocessing steps.
  • Recommendations for enhancing peptide search accuracy and efficiency.

Conclusions:

  • Effective bioinformatics analysis is crucial for interpreting complex MS-proteomics data.
  • Optimized data preprocessing and search engine parameters improve protein identification and quantification.
  • This chapter serves as a practical guide for researchers in MS-based proteomics.