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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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Related Experiment Video

Updated: Feb 25, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

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Informed-Proteomics: open-source software package for top-down proteomics.

Jungkap Park1, Paul D Piehowski1, Christopher Wilkins1

  • 1Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.

Nature Methods
|August 8, 2017
PubMed
Summary
This summary is machine-generated.

Top-down proteomics identifies intact proteins, but complex data requires advanced tools. Informed-Proteomics offers new algorithms for confident proteoform analysis, improving mass spectrometry data interpretation.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Top-down proteomics analyzes intact proteins, preserving critical information on modifications, isoforms, and processing.
  • Advances in instrumentation and sample preparation enhance top-down liquid chromatography-tandem MS (LC-MS/MS) data quality.
  • Top-down mass spectra present greater complexity compared to conventional bottom-up proteomics data.

Purpose of the Study:

  • To address the need for advanced algorithms and software for confident proteoform identification and quantification in top-down proteomics.
  • To introduce Informed-Proteomics, an open-source software suite designed for comprehensive top-down proteomics analysis.

Main Methods:

  • Development of an open-source software suite, Informed-Proteomics, comprising LC-MS feature-finding, database search, and results viewing algorithms.
  • Comparative analysis of Informed-Proteomics against other popular tools.
  • Utilized human-in-mouse xenograft luminal and basal breast tumor samples with known protein abundance differences.

Main Results:

  • Informed-Proteomics provides a new suite of tools for analyzing complex top-down mass spectrometry data.
  • The software facilitates confident proteoform identification and quantification.
  • Performance comparison demonstrated the utility of Informed-Proteomics on relevant biological samples.

Conclusions:

  • Informed-Proteomics is a valuable open-source resource for advancing top-down proteomics research.
  • The developed algorithms enhance the ability to interpret complex proteomic datasets, aiding in the study of protein variations.
  • The software supports more confident proteoform identification and quantification, crucial for understanding biological processes.