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Related Concept Videos

Proteomics01:33

Proteomics

7.9K
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...
7.9K

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Updated: Sep 12, 2025

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
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Assessing Long-Term Stored Tissues for Multi-Omics Data Quality and Proteogenomics Suitability.

Kyu Jin Song1,2, Minsuh Kim3, Yong Jin Heo4

  • 1Department of Applied Chemistry, Institute of Natural Science, Kyung Hee University, Yongin 17104, Republic of Korea.

Journal of Proteome Research
|August 10, 2025
PubMed
Summary

Archived cancer samples are viable for multiomics research. Long-term storage preserves essential genomic, transcriptomic, and proteomic data, enabling deeper insights into cancer biology and precision oncology.

Keywords:
bulk RNA sequencingcancer biologyfresh-frozen tissuemass spectrometrymultiomicsproteogenomicstargeted next generation sequencing

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Area of Science:

  • Oncology
  • Molecular Biology
  • Bioinformatics

Background:

  • Multiomics analyses are crucial for understanding cancer biology.
  • Sample availability is a significant challenge in multiomics research.
  • The impact of long-term storage on archived samples for multiomics is not well understood.

Purpose of the Study:

  • To assess the reliability of archived samples for multiomics studies.
  • To evaluate the effects of over a decade of storage on genomic, transcriptomic, and proteomic profiles.
  • To determine if archived samples can support cancer biology and precision oncology research.

Main Methods:

  • Comparative analysis of genomic, transcriptomic, and proteomic data from archived samples.
  • Assessment of gene expression patterns, protein stability, and post-translational modifications.
  • Evaluation of housekeeping genes/proteins and tissue-specific molecular differences.

Main Results:

  • Transcriptomic data showed reduced read counts but preserved core gene expression.
  • Proteomic measurements remained stable with minimal changes in post-translational modifications.
  • Housekeeping genes/proteins were consistent, and tumor-normal proteomic differences were retained.

Conclusions:

  • Archived samples stored for over a decade are suitable for multiomics research.
  • Long-term storage does not compromise essential molecular information for cancer studies.
  • Leveraging archived specimens can overcome sample limitations and advance precision oncology.