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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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Managing expectations when publishing tools and methods for computational proteomics.

Lennart Martens1,2, Oliver Kohlbacher3, Susan T Weintraub4

  • 1†Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.

Journal of Proteome Research
|March 13, 2015
PubMed
Summary
This summary is machine-generated.

Computational tools are essential for proteomics data analysis. This study proposes three manuscript types—Brief Communications, Research Articles, and Application Notes—to clarify tool maturity and aid researchers in selecting appropriate bioinformatics solutions.

Keywords:
bioinformaticscomputational mass spectrometrymanuscript types

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Computational tools are vital for analyzing complex proteomics data, including identification, quantification, and statistical assessment.
  • Selecting the appropriate computational tool is challenging due to the vast number of options and varying stages of tool development, especially for non-bioinformaticians.
  • Current publication practices can obscure the maturity and reliability of proteomics software, making it difficult for users to assess applicability.

Purpose of the Study:

  • To propose a standardized framework for organizing computational proteomics manuscripts.
  • To establish clear expectations for readers and reviewers regarding the maturity and scope of presented computational tools.
  • To facilitate the selection of appropriate bioinformatics tools for specific research needs.

Main Methods:

  • Community discussions with computational mass spectrometry experts.
  • Development of three distinct manuscript types: Brief Communications, Research Articles, and Application Notes.
  • Defining criteria for each manuscript type based on novelty, implementation maturity, and benchmarking.

Main Results:

  • Brief Communications: Suitable for novel computational approaches with early-stage implementations.
  • Research Articles: For presenting both novel concepts and mature, well-benchmarked implementations.
  • Application Notes: Ideal for showcasing mature, tested tools or concepts with improvements in quality, usability, or implementation.

Conclusions:

  • Organizing computational proteomics publications into these three types will streamline the review process.
  • This framework will help researchers quickly identify the maturity and suitability of tools for their specific workflows.
  • Standardized manuscript types enhance discoverability and usability of computational proteomics resources.