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Leveraging homologies for cross-species plasma proteomics in ungulates using data-independent acquisition.
Noor, Zainab; Paramasivan, Selvam; Ghodasara, Priya; Chemonges, Saul; Gupta, Rajesh; Kopp, Steven; Mills, Paul C; Ranganathan, Shoba; Satake, Nana; Sadowski, Pawel.
Afiliación
  • Noor Z; Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
  • Paramasivan S; School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia; Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia.
  • Ghodasara P; School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia; Veterinary Medicine, The University of Saskatchewan, Saskatchewan, SK, Canada.
  • Chemonges S; School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia; Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia.
  • Gupta R; Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia.
  • Kopp S; School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia.
  • Mills PC; School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia.
  • Ranganathan S; Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
  • Satake N; School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia; School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia.
  • Sadowski P; Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia. Electronic address: pawel.sadowski@qut.edu.au.
J Proteomics ; 250: 104384, 2022 01 06.
Article en En | MEDLINE | ID: mdl-34601153
The collection of blood plasma is minimally invasive, and the fluid is a rich source of proteins for biomarker studies in both humans and animals. Plasma protein analysis by mass spectrometry (MS) can be challenging, though modern data acquisition strategies, such as sequential window acquisition of all theoretical fragment ion spectra (SWATH), enable reproducible quantitation of hundreds of proteins in non-depleted plasma from humans and laboratory model animals. Although there is strong potential to enhance veterinary and translational research, SWATH-based plasma proteomics in non-laboratory animals is virtually non-existent. One limitation to date is the lack of comprehensively annotated genomes to aid protein identification. The current study established plasma peptide spectral repositories for sheep and cattle that enabled quantification of over 200 proteins in non-depleted plasma using SWATH approach. Moreover, bioinformatics pipeline was developed to leverage inter-species homologies to enhance the depth of baseline libraries and plasma protein quantification in bovids. Finally, the practical utility of using bovid libraries for SWATH data extraction in taxonomically related non-domestic ungulate species (giraffe) has been demonstrated. SIGNIFICANCE: Ability to quickly generate comprehensive spectral libraries is limiting the applicability of data-independent acquisition, such as SWATH, to study proteomes of non-laboratory animals. We describe an approach to obtain relatively shallow foundational plasma repositories from domestic ruminants and employ homology searches to increase the depth of data, which we subsequently extend to unsequenced ungulates using SWATH method. When applied to cross-species proteomics, the number of proteins quantified by our approach far exceeds what is traditionally used in plasma protein tests.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteoma / Proteómica Límite: Animals Idioma: En Revista: J Proteomics Asunto de la revista: BIOQUIMICA Año: 2022 Tipo del documento: Article País de afiliación: Australia Pais de publicación: Países Bajos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteoma / Proteómica Límite: Animals Idioma: En Revista: J Proteomics Asunto de la revista: BIOQUIMICA Año: 2022 Tipo del documento: Article País de afiliación: Australia Pais de publicación: Países Bajos