A major challenge of mass spectrometry is data analysis. Capitalizing upon the Canary Centers bioinformatics resources, data generated by the proteomics core facility is archived and analyzed on a Dell Cluster housed in the core facility. This cluster provides 128TB of RAID storage, an 80 node computing cluster and web, database and file conversion servers. Users of the facility have convenient access to an easy-to-use, web-accessible, automated data analysis pipeline developed by Dr. Parag Mallick (based upon ProteoWizard and LabKey Server). Dr. Mallick is the principle investigator of the ProteoWizard projecta large software initiative that develops software for the analysis of mass spectrometry data. In 2013 alone, ProteoWizard was downloaded more than 42,000 times and is in use in labs across the world.
Proteomics Core Facility Description
The following description is suitable for use in conjunction with grant proposals:
The Proteomics Core Facility associated with the Canary Center at Stanford for Cancer Early Detection is a shared resource facility that supports Canary Center faculty, associates, and Canary Foundation science teams. The goal of the core facility is to enable a diverse group of investigators to leverage mass spectrometry in support of their research. This is accomplished through training and subsequent access to mass spectrometers at limited cost to Canary Center faculty, affiliates and their trainees. At present, the core facility supports four mass spectrometers including:
- Thermo Orbitrap Elite with ETD detector;
- Thermo LTQ Orbitrap Velos;
- Agilent 6490 triple quadrupole LC/MS; and
- AB SCIEX 5800 TOF/TOF (MALDI) systems.
Other instruments available in the MS Core include an Agilent AssayMAP Bravo liquid-handing robotic system and a Biacore X100 bimolecular interaction system. The core facility occupies over 2200 sq. ft. and the central room is designed to support ten LC-MS/MS systems including as many as six large LTQ Orbitrap-like systems. There are access panels in proximity to each mass spectrometer that provide nitrogen, UHP helium, compressed air, and an extractor for removal of vacuum pump fumes. Uninterrupted power supply (UPS) systems and an emergency backup generator support all mass spectrometers, HPLCs and computers. Adjacent to the central room is a sample preparation room (with balances, fume hood and water system) and a utility room (with flammable solvent storage and switching systems for nitrogen and UHP helium). An additional lab supports a MALDI mass spectrometer and instruments associated with MALDI applications including LC-MALDI and MALDI imaging mass spectrometry. A major challenge of mass spectrometry is the analysis of the data. Capitalizing upon the Canary Center's bioinformatics resources, data generated by the Proteomics Core Facility is archived and analyzed on a Dell Cluster housed within the Canary Center. This cluster provides 128TB of RAID storage, an 80 node computing cluster and web, database and file conversion servers. Users of the facility have convenient access to an easy-to-use, web-accessible, automated data analysis pipeline developed by Dr. Mallick (based upon ProteoWizard and LabKey Server).