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Related Concept Videos

Proteomics01:33

Proteomics

7.6K
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

Peptide Identification Using Tandem Mass Spectrometry

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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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Updated: Aug 14, 2025

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.

Eric W Deutsch1, Luis Mendoza1, David D Shteynberg1

  • 1Institute for Systems Biology, Seattle, Washington 98109, United States.

Journal of Proteome Research
|January 17, 2023
PubMed
Summary

The Trans-Proteomic Pipeline (TPP) is a 20-year-old mass spectrometry data analysis suite. Its latest release offers advanced tools for protein identification and quantification, deployable across diverse computing platforms.

Keywords:
6.1.0 ParhelionPeptideProphetProteinProphetTrans-Proteomic Pipelinecomputational proteomicsmass spectrometryproteomics

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • The Trans-Proteomic Pipeline (TPP) has evolved over 20 years, starting with PeptideProphet and ProteinProphet.
  • It is a comprehensive mass spectrometry data analysis suite with continuous development.

Purpose of the Study:

  • To present the latest information on TPP tools and their capabilities.
  • To detail TPP's deployment options across various computing environments.
  • To highlight TPP's utility through tutorials and synergistic projects.

Main Methods:

  • Utilizes machine learning for data analysis and robust statistical modeling.
  • Offers tools for spectrum processing, searching, validation, abundance computation, and protein inference.
  • Supports deployment on Windows, Linux clusters, and cloud computing platforms.

Main Results:

  • The current TPP release provides a wide array of tools for comprehensive mass spectrometry data analysis.
  • Machine learning is integrated to maximize information extraction and ensure data accuracy.
  • TPP is adaptable for use on personal computers to large-scale cloud environments.

Conclusions:

  • TPP remains a vital and evolving resource for mass spectrometry data analysis.
  • Its flexibility and advanced features support diverse research needs.
  • Future development plans aim to further enhance TPP's capabilities.