Stable isotope labelling in zebrafish allows in vivo monitoring of cardiac morphogenesis

Quantitative proteomics is an important tool to study biological processes but so far has been challenging to apply to the zebrafish. Here, we describe a large-scale quantitative analysis of the zebrafish proteome using a combination of stable isotope labeling (SILAC) and liquid chromatography mass spectrometry (LC-MS). Unsaturated SILAC-labeling was employed to determine protein turnover rates in different tissues and allowed identification of newly synthesized proteins during fin regeneration. Proteins derived from the fully labeled fish were used as a standard to quantify changes during embryonic heart development. LC-MS assisted analysis of the proteome of ALCAM (activated leukocyte cell adhesion molecule) zebrafish morphants revealed a down-regulation of components of the network required for cell adhesion and maintenance of cell shape as well as secondary changes due to arrest of cellular differentiation. Quantitative proteomics in zebrafish using the SILAC technique provides an unprecedented resource to study developmental and regenerative processes in zebrafish.