Quantitative proteomics is an important tool to study biological processes, but so far it has been challenging to apply to zebrafish. Here, we describe a large scale quantitative analysis of the zebrafish proteome using a combination of stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS). 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 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 stable isotope-labeling technique provides an unprecedented resource to study developmental processes in zebrafish. Over the past years, mass spectrometry-based proteomics has been widely used to analyze complex biological samples (1). Although the latest generation of MS instrumentation allows proteome-wide analysis, protein quantitation is still a challenge (2, 3). Metabolic labeling using stable isotopes has been used for almost a century. Today, the most commonly used techniques for relative protein quantification are based on 15 N labeling and stable isotope labeling by amino acids in cell culture (SILAC) 1 (4, 5). SILAC was initially developed for cell culture experiments, and recent approaches extended labeling to living organisms, including bacteria (6), yeast (7), flies (8), worms (9), and rodents (10, 11). In addition, several pulsed SILAC (also known as dynamic SILAC) experiments were performed to assess protein dynamics in cell culture and living animals (12-15).The zebrafish (Danio rerio) has proved to be an important model organism to study developmental processes. It also serves as a valuable tool to investigate basic pathogenic principles of human diseases such as cardiovascular disorders and tissue regeneration (16). So far, most researchers rely on immunohistochemistry and Western blots for semiquantitative protein analysis, an approach that is hampered by the paucity of reliable antibodies in zebrafish. Proteomics approaches that depend on two-dimensional gel approaches (17-19) have not gained wide popularity because of issues with workload, reproducibility, and sensitivity (20, 21).Another approach for protein quantitation is the chemical modification of peptides, and so far several isobaric tagging methods, including ICAT (22), iTRAQ (23),18 O (24), and dimethyl labeling (25), have been proven to be successful methods.Recently, a quantitative phosphopeptide study based on dimethyl labeling in zebrafish showed the consequences of a morpholino-based kinase knockdown (26). However, each chemical modification bears the risk of nonspecific and incomplete labeling, which complicates mass spectrometric data interpretation.Alternatively, a metabolic labeling study with stable isotopes was recently performed on adult zebrafish by the admi...