With the global consumption of fish outpacing population growth, aquaculture sector is facing challenges to address the rising demand of food and nutritional security. Integrative omics research provides a strong platform to understand the basic biology and translate this knowledge into sustainable solutions in tackling disease outbreak, increasing productivity thus ensuring food security. To further understand the complex biology of host-pathogen response and support the aquaculture effort, genome and proteome reference maps moving beyond simple sequence information of cultivated fish species will accelerate research and translation of quality products for food industries. Towards this end, we have performed an extensive proteomics-based investigation of Labeo rohita, one of the economically important fish species produced in world aquaculture. Deep proteomic profiling of 17 histologically normal tissues, plasma and embryo provided mass-spectrometric evidence for 6015 high confident canonical proteins at 1% false discovery rate. Tissue enriched expression of several biologically important proteins was validated using targeted proteomics with high quantitative accuracy. We characterised the global post translational modifications (PTMs) in terms of acetylation (n-terminus and lysine), methylation (n-terminus, lysine and arginine) and phosphorylation (serine, threonine and tyrosine) to present a comprehensive proteome resource. An interactive web-based portal was developed to support the Labeo rohita PeptideAtlas, (www.peptideatlas.org), a unique community resource for mass spectrometry-based peptide/protein evidence in fish. This draft proteome map of Labeo rohita would advance basic and applied research in aquaculture to meet the most critical challenge of providing food and nutritional security to an increasing world population.