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Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)
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  • Dietmar Kültz,
  • Alison M. Gardell,
  • Anthony De Tomaso,
  • Greg Stoney,
  • Baruch Rinkevich,
  • Yuval Rinkevich,
  • Andy Qarri,
  • Weizhen Dong,
  • Brenda Luu,
  • Mandy Lin
Dietmar Kültz
University of California Davis

Corresponding Author:dkueltz@ucdavis.edu

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Alison M. Gardell
University of Washington Tacoma
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Anthony De Tomaso
University of California Santa Barbara
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Greg Stoney
University of California Santa Barbara
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Baruch Rinkevich
National Institute of Oceanography
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Yuval Rinkevich
Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt
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Andy Qarri
National Institute of Oceanography
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Weizhen Dong
University of California Davis
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Brenda Luu
University of California Davis
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Mandy Lin
University of California Davis
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Abstract

Botryllus schlosseri, is a model marine invertebrate for studying immunity, regeneration, and stress-induced evolution. Conditions for validating its predicted proteome were optimized using nanoElute® 2 deep-coverage LCMS, revealing up to 4,930 protein groups and 20,984 unique peptides per sample. Spectral libraries were generated and filtered to remove interferences, low-quality transitions, and only retain proteins with >3 unique peptides. The resulting DIA assay library enabled label-free quantitation of 3,426 protein groups represented by 22,593 unique peptides. Quantitative comparisons of a laboratory-raised with two field-collected populations revealed (1) a more unique proteome in the laboratory-raised population, and (2) proteins with high/low individual variabilities in each population. DNA repair/replication, ion transport, and intracellular signaling processes were unique in laboratory-cultured colonies. Spliceosome and Wnt signaling proteins were the least variable (highly functionally constrained) in all populations. In conclusion, we present the first colonial tunicate’s deep quantitative proteome analysis, identifying functional protein clusters associated with laboratory conditions, different habitats, and strong versus relaxed abundance constraints. These results empower research on B. schlosseri with proteomics resources and enable quantitative molecular phenotyping of changes associated with transfer from in situ to ex situ and from in vivo to in vitro culture conditions.
Submitted to PROTEOMICS
30 Jan 2024Review(s) Completed, Editorial Evaluation Pending
30 Jan 20241st Revision Received
12 Feb 2024Editorial Decision: Accept