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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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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Updated: Jan 9, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Profiler: an open web platform for multi-omics analysis.

Yanis Zirem1, Léa Ledoux1, Isabelle Fournier1,2

  • 1Univ. Lille, Inserm, CHU Lille, U1192, Protéomique Réponse Inflammatoire Spectrométrie de Masse, PRISM, Lille F-59000, France.

Bioinformatics (Oxford, England)
|December 1, 2025
PubMed
Summary
This summary is machine-generated.

Profiler is a new open-source platform simplifying complex multi-omics data analysis. It integrates various tools for reproducible research, making advanced computational biology accessible for precision medicine.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • High-throughput multi-omics technologies generate large, heterogeneous datasets.
  • Existing bioinformatics tools are fragmented, hindering reproducibility and accessibility.
  • A need exists for an integrated, user-friendly, scalable platform for multi-omics analysis.

Purpose of the Study:

  • To present Profiler, an open-source, modular platform for unified multi-omics data analysis.
  • To provide a user-friendly interface for complex computational biology tasks.
  • To democratize multi-omics analysis for systems biology and precision medicine.

Main Methods:

  • Profiler is a Python-based platform utilizing Streamlit for a web and desktop interface.
  • It integrates data import, quality control, preprocessing, statistical testing, machine learning, and deep learning.
  • Supports diverse omics modalities: proteomics, transcriptomics, lipidomics, and electroencephalogram (EEG) data.

Main Results:

  • Profiler unifies diverse analytical workflows within a single reproducible environment.
  • Applications demonstrated reproducible identification of molecular subtypes and potential therapeutic targets.
  • Generated fully traceable analysis reports rapidly for glioblastoma and pancancer datasets.

Conclusions:

  • Profiler democratizes multi-omics analysis by integrating advanced analytics into an intuitive interface.
  • It offers a robust, scalable foundation for systems biology and precision medicine research.
  • The platform enhances accessibility and reproducibility in complex biological data analysis.