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Related Concept Videos

Proteomics01:33

Proteomics

10.2K
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...
10.2K

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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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ProCon - PROteomics CONversion tool.

Gerhard Mayer1, Christian Stephan2, Helmut E Meyer3

  • 1Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany.

Journal of Proteomics
|July 18, 2015
PubMed
Summary
This summary is machine-generated.

Proteomics data requires standardized formats for public repositories. The ProCon tool converts proprietary data into mzIdentML and PRIDE XML, aiding researchers in data sharing and computational proteomics.

Keywords:
Conversion toolPRIDEProConProteomeXchangeProteomicsmzIdentML

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Science

Background:

  • Increasing proteomics experimental data necessitates public data sharing.
  • Journal requirements mandate data availability in public repositories.
  • Standardized data formats are crucial for proteomics data integration and analysis.

Purpose of the Study:

  • To address the need for user-friendly conversion tools for proteomics data.
  • To facilitate the upload of proteomics identification data into public repositories.
  • To support wet-lab scientists in preparing data for public sharing.

Main Methods:

  • Development of ProCon, a Java-based conversion tool.
  • Conversion of proteomics identification data into mzIdentML and PRIDE XML formats.
  • Support for various input formats including Sequest™/Comet .out, ProteomeDiscoverer® 1.x, and ProteinScape®.

Main Results:

  • ProCon enables conversion of proprietary proteomics search results into standard formats.
  • The tool supports popular software and LIMS systems.
  • Facilitates compliance with data sharing mandates in proteomics research.

Conclusions:

  • ProCon provides a valuable solution for standardizing proteomics data.
  • The tool enhances data accessibility and reusability in computational proteomics.
  • Promotes wider adoption of standardized formats in the proteomics community.