The Chromosome-centric Human Proteome Project (C-HPP) aims to systematically map 
the entire human proteome with the intent to enhance our understanding of human 
biology at the cellular level. This project attempts simultaneously to establish 
a sound basis for the development of diagnostic, prognostic, therapeutic, and 
preventive medical applications. In Iran, current efforts focus on mapping the 
proteome of the human Y chromosome. The male-specific region of the Y chromosome 
(MSY) is unique in many aspects and comprises 95% of the chromosome's length. 
The MSY continually retains its haploid state and is full of repeated sequences. 
It is responsible for important biological roles such as sex determination and 
male fertility. Here, we present the most recent update of MSY protein-encoding 
genes and their association with various traits and diseases including sex 
determination and reversal, spermatogenesis and male infertility, cancers such 
as prostate cancers, sex-specific effects on the brain and behavior, and 
graft-versus-host disease. We also present information available from RNA 
sequencing, protein-protein interaction, post-translational modification of MSY 
protein-coding genes and their implications in biological systems. An overview 
of Human Y chromosome Proteome Project is presented and a systematic approach is 
suggested to ensure that at least one of each predicted protein-coding gene's 
major representative proteins will be characterized in the context of its major 
anatomical sites of expression, its abundance, and its functional relevance in a 
biological and/or medical context. There are many technical and biological 
issues that will need to be overcome in order to accomplish the full scale 
mapping.