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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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A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
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Computational proteomics tools for identification and quality control.

Dominik Kopczynski1, Albert Sickmann2, Robert Ahrends1

  • 1Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.

Journal of Biotechnology
|July 6, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces computational proteomics tools, SearchGUI and PeptideShaker, for protein identification and quantification. These services enhance proteomics data analysis and offer a spectral library for targeted proteomics validation.

Keywords:
Computational proteomicsPeptide identificationPeptide spectra library databaseProtein inference

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Proteomics

Background:

  • Proteomics experiments require robust computational tools for data analysis, including protein identification, quantification, and validation.
  • The German network for bioinformatics infrastructure (de.NBI) provides essential bioinformatics services and software platforms.

Purpose of the Study:

  • To present integrated computational tools (SearchGUI and PeptideShaker) for proteomics data analysis.
  • To introduce a web service for scalable protein identification and a database for targeted proteomics.
  • To offer user-friendly and high-quality bioinformatics solutions for proteomics researchers.

Main Methods:

  • Utilized SearchGUI to manage multiple search engines for peptide-spectrum matching in MS2 measurements.
  • Employed PeptideShaker to consolidate matches, generate consensus protein lists, and provide statistical confidence.
  • Developed a web service for protein identification and a spectral library database for targeted proteomics.

Main Results:

  • SearchGUI and PeptideShaker effectively identify and quantify proteins from mass spectrometry data.
  • A scalable web service for protein identification using Docker is planned.
  • A user-friendly web service database with high-resolution spectral data for targeted proteomics is available.

Conclusions:

  • The presented tools and services significantly improve computational proteomics workflows.
  • Future development includes a scalable web service for enhanced protein identification.
  • Accessible spectral data facilitates targeted proteomics analyses and validation.