Global Protein Expression Profiling of Zebrafish Organs Based on in Vivo Incorporation of Stable Isotopes

The zebrafish has become a widely
used model organism employed
for developmental studies, live cell imaging, and genetic screens.
High-resolution transcriptional profiles of different developmental
and adult stages of the fish and of its various organs were generated,
which are readily accessible via the ZFIN database. In contrast, quantitative
proteomic studies of zebrafish organs are still in their infancy.
Here, we used the SILAC (stable isotope labeling by amino acids in
cell culture) zebrafish as a “spike-in” reference to
generate a protein atlas of nine organs including gills, brain, heart,
muscle, liver, spleen, skin, swim bladder, and testis. Single-shot
4 h LC gradients coupled to a Quadrupole-Orbitrap (QExactive) instrument
allowed identification of over 5000 proteins in less than 5 days,
of which more than 70% were quantified in triplicate. Identified proteins
were subjected to BLAST searches and Gene Ontology classification
to improve annotation of zebrafish proteins and obtain insights into
potential functions. Comparison to mouse tissue proteome data sets
revealed differences and similarities in the protein composition of
zebrafish versus mouse organs. We reason that the data set will be
helpful for the proteomic characterization of zebrafish organs and
identification of tissue-specific proteins that might serve as biomarkers.
Our approach provides a complementary view into the biochemistry of
zebrafish models and will assist large-scale protein quantification
in zebrafish disease models.