Second Generation Proteomics, Phoenix Project and CNHPP
Jun Qin
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, P. R. China, 102206
Department of Biochemistry and Molecular Biology and Department of Molecular and Cellular Biology, Baylor
College of Medicine, Houston, TX77030, USA
As the performance of mass spectrometer (MS) and large-scale protein sequencing has been improved
over the last few years, pushing the proteome analysis to the level that is compatible to mRNA-seq.
The development of affinity-based reagents that target sub-proteomes that may correlate with activities,
such as transcription factor (TF) DNA binding activity and post-translational modification (PTM)
(especially for phosphorylation, ubiquitilation, and acetylation) has further extended proteomics to low
abundant but functionally important proteins. Coupling with a fast screening (Fast-seq) approach
developed recently, proteomics nowadays can achieve dual high-throughput in both number of protein
identification and number of sample measured. Now it seems that proteomics has established its
technology platforms to rival genomics and transcriptomics.
China is at the leading edge of catching the wave of rapid development in proteomics. A National
Center for Protein Sciences (dubbed the Phoenix project) is under construction and due to open in
October, 2015. This center is filled with cutting edge proteomics technologies and state-of-the-art
proteomics instruments. It has the capacity of measuring 10 proteomes per day when it is in operation.
Such an analysis power will be shared with scientists working on proteins, biology and medicine in
China and the world.
Last year, Ministry of Science and Technology approved the Chinese Human Proteome Project
(CNHPP). This is a large undertaking at dissection of the proteomic landscape of cancer. Alteration of
Signaling pathways in 10 cancers that have major impacts in health and economy in China will be
mapped through the collective efforts of more than 40 labs in China.
Proteomics has the ability to catch dynamic pathways that response to biological processes, especially
for PTM-dependent signal transductions, transcription factor activity related transcriptional regulation,
and protein-protein interactions (PPI). Proteomics sets itself apart from other omics that it offers
multi-dimensional data and provides direct information on what is happening inside the cell. I will
summarize recent development and current capability of proteomics for biological research and discuss
future direction of proteomics for translational medicine.