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\begin{document}

\title{Deep quantitative proteomics of North American Pacific coast star
tunicate (\emph{Botryllus schlosseri})}



\author[1]{Dietmar Kültz}%
\author[2]{Alison M. Gardell}%
\author[3]{Anthony De Tomaso}%
\author[3]{Greg Stoney}%
\author[4]{Baruch Rinkevich}%
\author[5]{Yuval Rinkevich}%
\author[4]{Andy Qarri}%
\author[1]{Weizhen Dong}%
\author[1]{Brenda Luu}%
\author[1]{Mandy Lin}%
\affil[1]{University of California Davis}%
\affil[2]{University of Washington Tacoma}%
\affil[3]{University of California Santa Barbara}%
\affil[4]{National Institute of Oceanography}%
\affil[5]{Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt}%


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  \date{May 17, 2024}


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\begin{abstract}
\emph{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\selectlanguage{ngerman}® 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 \textgreater{}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 \emph{B. schlosseri} with proteomics
resources and enable quantitative molecular phenotyping of changes
associated with transfer from \emph{in situ} to \emph{ex situ} and from
\emph{in vivo} to \emph{in vitro} culture conditions.%
\end{abstract}\selectlanguage{ngerman}%



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\verb`Manuscript Bosch proteomics 02Dec23.docx`  available at \url{https://authorea.com/users/376229/articles/736081-deep-quantitative-proteomics-of-north-american-pacific-coast-star-tunicate-botryllus-schlosseri}

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