Overview

Systems Biology

The National Institutes of Health has defined Systems Biology as a study of systems of biological components, which may be molecules, cells, organisms or entire species ( http://irp.nih.gov/catalyst/v19i6/systems-biology-as-defined-by-nih). Living systems are dynamic and complex and their behavior may be hard to predict from the properties of individual parts. The Proteomics and Systems Biology Core Facility provides technology to investigators, which permits the characterization and quantification of proteins and metabolites to enable the development of models that predict the dynamic behavior of living systems. There are currently three mass spectrometry-based services available in the Core - Proteomics, Metabolomics, and Biomarker.

Core Operation

Dr. Blair, the Scientific Director, is responsible for the overall direction of the Core and Dr. Yuan, the Technical Director provides scientific consultation about applications of the Core services. Dr. Yuan is responsible for the day-to-day operations of the Core, supervising the technical staff, and monitoring quality control. Drs. Blair and Yuan assist investigators in evaluating the potential utility of proteomics, metabolomics, and biomarker methodology and help in the design of research projects that effectively and appropriately incorporate such methodology. The Core provides cost-effective access for investigators to expensive and highly technical services that are not commonly available in individual departments and laboratories.

Proteomics

Mass spectrometry instrumentation available:

Thermo Scientific LTQ Orbitrap-XL equipped with Waters nanoAcquity LC system; Thermo Scientific LTQ-XL equipped with Eksigent nano LC-2D; Thermo Scientific LTQ equipped with Eksigent nano LC-2D; Thermo Scientific TSQ Quantum triple quadrupole mass spectrometer equipped with Waters 2690 Series LC system.

Both nanoflow and microflow liquid chromatography-mass spectrometry (LC-MS) and LC-tandem MS (MS/MS) analyses can be conducted after protease digestion of proteins or complex mixtures of proteins. Quantification of individual peptides can then be performed using LC-multiple reaction monitoring (MRM)/MS. This can be implemented using label-free methods or by the use of more rigorous stable isotope dilution methodology based on stable isotope labeling by amino acids in cell culture (SILAC) as described by Ong and Mann (Nat Protoc. 2006;1:2650-2660).

Additional services are available for conducting 2D Gel electrophoresis of proteins on large format gels (26 x 20 cm) or small format gels (8 x 10 cm) together with SYPRO Ruby Staining and Scanning, and Cy2,3,5 Dye labeling and Scanning.

Metabolomics

Mass spectrometry instrumentation available:

Thermo Scientific LTQ Orbitrap-XL equipped with nanoAcquity LC system; AB Sciex API-4000 equipped with Agilent 1100 Series LC system.

The Thermo Orbitrap instrument allows high-resolution nanoflow LC-MS to be conducted on samples from control and experimental studies. Differentially expressed metabolites can then be identified using Thermo Scientific Sieve software. Quantification is performed using LC-selected reaction monitoring (SRM)/MS. This can be implemented either by label-free methods or by the use of more rigorous stable isotope dilution methodology such as stable isotope labeling by essential nutrients in cell culture (SILEC) as described recently by Basu and Blair (Nat Protoc. 2012;7:1-12).

Biomarker

Mass spectrometry instrumentation available:

Thermo Scientific TSQ Quantum triple quadrupole mass spectrometer equipped with Waters 2690 LC system; Agilent 6460 triple quadrupole mass spectrometer equipped with Agilent 1200 series LC system.

Rigorous quantification of serum, plasma or urinary biomarkers identified by metabolomics studies can be conducted using stable isotope dilution LC-SRM/MS methodology as described by Ciccimaro and Blair (Bioanalysis. 2010;2:311-341). The Core services are normally utilized for biomarker validation studies, for disease diagnosis, for detecting the adverse effects of environmental chemicals, or for monitoring the effect of therapeutic agents.

Contact Information

Chao-Xing Yuan, Ph.D.  yuancx@upenn.edu

The Proteomics Facility Office
838 Biomedical Research Building II/III
Philadelphia, PA 19104-6160

(215) 573-9883 Ph.
(215) 573-9889 Fax