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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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Proteomics Using Draft Genomes: A Case Study in Spotted Hyena.

David L Tabb1,2, Aidan Swartz1, Roxanne L Higgitt1

  • 1South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.

Journal of Proteome Research
|January 9, 2026
PubMed
Summary
This summary is machine-generated.

The 2022-Shao spotted hyena genome assembly is superior for proteomic analysis, identifying more spectra and revealing significant orthology with domestic cat proteomes. This research advances spotted hyena (Crocuta crocuta) molecular biology and comparative genomics.

Keywords:
genome annotationlymphatic systemnonmodel organismswildlife

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Area of Science:

  • Genomics and Proteomics
  • Comparative Molecular Biology
  • Mammalian Evolutionary Biology

Background:

  • The spotted hyena (Crocuta crocuta) exhibits unique hunting behaviors, alternating between social clan life and solitary hunting.
  • Limited genomic data previously hindered molecular biology studies of C. crocuta.
  • Recent advancements include three draft genomes (2020-Yang, 2022-Shao, 2023-DNA Zoo) and generated RNA-Seq and proteomics data.

Purpose of the Study:

  • To evaluate the effectiveness of different Crocuta crocuta draft genome assemblies for proteomic identification.
  • To compare the proteomic identification capabilities of C. crocuta databases against homologous species.
  • To identify differential proteins within C. crocuta lymph nodes.

Main Methods:

  • Evaluation of three draft genomes (2020-Yang, 2022-Shao, 2023-DNA Zoo) and a Trinity de novo assembly (2017-SUN) using RNA-Seq data.
  • Annotation completeness assessed by BUSCO; RNA-Seq read alignment by Salmon.
  • Protein sequence database comparison using Proteinortho and FragPipe for LC-MS/MS data analysis against C. crocuta, Felis catus, Canis lupus familiaris, and Mus musculus databases.

Main Results:

  • The 2022-Shao assembly identified 15.6% more spectra than the 2020-Yang reference proteome.
  • The Felis catus (domestic cat) protein database showed high orthology, identifying 80.5% as many spectra as the 2020-Yang database, reflecting shared ancestry within Feliformia.
  • Over 1000 protein sequences were lost when using the 2020-Yang database compared to others; FragPipe analysis of the 2022-Shao assembly revealed significant orthology with F. catus organ proteomes.

Conclusions:

  • The 2022-Shao draft genome assembly is a more effective resource for C. crocuta proteomic studies than the 2020-Yang assembly.
  • Comparative proteomic analysis highlights substantial evolutionary conservation between spotted hyena and domestic cat organ proteomes.
  • This study provides foundational proteomic data for C. crocuta, including insights into differential protein expression in various lymph node regions.