U.S. Department of Energy

Pacific Northwest National Laboratory

Wei-Jun Qian


Dr. Wei-Jun Qian is a bioanalytical chemist whose research centers primarily on the development and applications of mass spectrometry-based approaches for better quantify the dynamic changes in protein abundances and protein post-translational modifications in biological and clinical applications. Dr. Qian is currently a Staff Scientist at the Integrative Omics group in the Biological Sciences Division at PNNL, where he has worked since 2002.  Dr. Qian has received several prestigious honors, including a National Institutes of Health Director’s New Innovator Award (2009), and a Presidential Early Career Award for Scientists and Engineers (PECASE) in 2011.  His current research involves the development of chemical proteomic approaches for site-specific quantification of cysteine-based redox modifications and more sensitive selected reaction monitoring (SRM)-based targeted quantification techniques with applications in pancreatic islets, diabetes, and oxidative stress-related disease areas. In addition to research, Dr. Qian is actively involved in training and mentoring postdoctoral researchers and intern students.


Research Interests:


Our research team primarily focuses on the development of novel and improved proteomics approaches to enable the study of signaling transduction mechanisms and the identification of key functional molecular targets of biological systems.  Our developments are centered on the goal of achieving accurate global and targeted analysis and quantification of proteins, protein isoforms, and posttranslational modifications (PTMs). For protein PTMs, we are particularly interested in redox modifications on protein thiols and their potential crosstalk with other types of PTMs such as phosphorylation as a basis mechanism of signaling regulation and dysregulation. For targeted quantification, we are developing highly sensitive technologies to enable the detection of extreme low-abundance proteins for biomarker discovery and systems biology applications on specific signaling networks such as epidermal growth factor receptor (EGFR) network. The applications included both health-related areas such as diabetes, insulin resistance, redox biology, and biomarker discovery, and energy and enviromental related areas such as redox and PTMs in microbial organisms.

Targeted Proteomics

Besides global proteomics, targeted proteomics using selected reaction monitoring or other data-independent acquistion modes has become increasingly important and popular for achieving accurate absolute or relative quantification of low-abundance proteins, protein isoforms, and PTMs to eluciate specific pathways or networks in systems biology applications or for verification of candidate biomarkers in specific diseases such as cancer or diabetes. Under the support of NIH Director's New Innovator Award, we have recently developed an ultra-sensitive targeted proteomics technology termed high-pressure high-resolution separations with intelligent selection and multiplexing (PRISM) (Fig. 1).  PRISM-SRM enables the detection of proteins in blood plasma as low as 50-100 pg/mL and low-abundance cellular proteins in low 100s copies per cell.  PRISM also enables the direct quantification of PTMs and their stoichiometries without affinity enrichment.  Currently, we are applying targeted quantification to biomarker verification, signaling network quantification, and PTM quantification studies


Redox Regulation and Redox PTMs on Protein Thiols

Redox regulation represents a fundamental process in all organisms and plays a multifaceted role in signal transduction, metabolism, and transcription with cellular redox homeostasis as an “integrator” of information from metabolism and the environment. The role of redox regulation and oxidative stress from microbes, plants, mammalian organisms, and diseases are increasingly recognized. Protein cysteine thiols serve as a major type of redox switches in signaling transduction in cells (Fig.2). We focus on developing quantitative thiol-based redox proteomics approaches to enable the identification and quantification of different redox PTMs at the proteome level (Fig.3). These approaches have enabled studies in the role of S-nitrosylation, S-glutathionylation, or general thiol-oxidation relevant to cellular metabolism and oxidative stress in microbes and mammalian cells and tissues. Interested application areas included cyanobacteria related to biofuel research, ageing related diseases, and cancer. A future direction will be the investigation of crosstalk between different PTMs in signaling pathways.

  • Ph.D. Bioanalytical Chemistry, University of Florida, Gainesville, FL
  • M.S. Analytical Chemistry, Nanjing Univeristy, Nanjing, China
  • B.S. Chemistry, Nanjing University, Nanjing, China
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