Proteomics is the study of proteins and their interactions in a cell. Though proteome reflects more accurately on the dynamic state of a cell, tissue, or organism, much is expected from proteomics to yield better disease markers for diagnosis and therapy monitoring. The advent of proteomics technologies for global detection and quantitation of proteins creates new opportunities & challenges for those seeking to gain greater understanding of diseases. High-throughput proteomics technologies combining with advanced bioinformatics are extensively used to identify molecular signatures of diseases based on protein pathways & signaling cascades. Mass spectrometry plays a vital role in proteomics and has become an indispensable tool for molecular & cellular biology. While the potential is great, many challenges and issues remain to be solved, such as mining low abundant proteins & integration of proteomics with genomics & metabolomics data. Nevertheless, proteomics is the foundation for constructing and extracting useful knowledge to biomedical research.