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Resources: Proteomics Platform

The Proteomics laboratory at the Broad Institute consists of approximately 5,047 sq. ft. of wet chemistry and instrument lab space located in the 415 Main St. building, floor 5. The laboratory is exceptionally well equipped.  The facilities house a number of state-of-the-art mass spectrometry systems, including eight ultra-high performance LC-MS/MS instruments from Thermo (5 Q-Exactive Plus, 1 Q-Exactive HF, 1 LTQ-Orbitrap Elite and our newest instrument a Orbitrap Fusion Lumos Tribrid Mass Spectrometer). For targeted, quantitative analysis by MRM/SRM the group has three triple quadrupole LC-MS/MS systems: AB/Sciex 5500, Waters Xevo-TQS and Thermo TSQ Quantiva. Each of the LC-MS/MS systems is equipped with an ultra-high performance nanoflow HPLC system (5 EASY nLC 1200, 4 EASY nLC 1000, 1 NanoAcquity, 1 Eskigent nanoLC) for routine nanoscale chromatography with heated columns (20-50cm length, 75um id, <2uM particle size). In addition, we have a full complement of analytical scale to nano-scale liquid chromatography systems for protein and peptide fractionation available, as well as conventional protein biochemistry and lipid and small molecule laboratory kits such as gel electrophoresis systems and centrifuges. We have a dedicated tissue culture facilities for growing cells for quantitative studies via SILAC metabolic profiling and full BL2 capabilities for biological and clinical sample preparation.  For automation we have three Agilent Bravo robots, 2 of which have AssayMap heads for microchromatography-assisted sample preparation; one Thermo Kingfisher 96 robot; and a Perkin Elmer Janus Automated Workstation.

To support the data analysis for the various discovery projects in the proteomics platform Spectrum Mill is installed and currently run on 4 Virtual Servers (see section Computational – Shared Resource section below for hardware and staffing description) each running Windows 2012 Server virtualized via VMware. Each server is configured with 8 or 12 processors, 24 or 56 GB RAM, and 1 or 2TB of storage. For SILAC datasets, MaxQuant is similarly installed and can run on up to 8 dynamically instantiated virtual servers (each with 8 CPU, 16 GB RAM, and 128 GB local storage; accompanied by 7 TB network attached storage shared by all). Because of the virtualization, adding capacity by way of additional servers or increased CPU, RAM, or storage are easily accomplished with a few hours notice since the Proteomics compute needs are small relative to the institutional infrastructure in place to handle the huge compute requirements of our Genomics platform for sequencing. Raw data from all mass spectrometers is automatically backed up and archived to network-attached storage with current consumption of 65 TB (from years 2004-2015).

The Proteomics platform currently has 31 scientists, including 6 postdoctoral associates, 11 highly experienced Ph.D. or Ph.D. equivalent staff, and 14 technical staff.  The technical staff is largely comprised of recent college graduates who train and stay for a period of 2-3 years before going off to graduate school or medical school.  In addition the group has two seasoned administrative personnel that handle grants and collaborative interactions with the greater Broad community of over 1500 scientists.