You are here

Proteomics Facility

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 and HPLCs, including:

  • ultra-high performance LC-MS/MS (Thermo Q-Exactive Plus, Q-Exactive HF, Q-Exactive HF-X, Orbitrap Fusion Lumos Tribrid Mass Spectrometer, multiple Orbitrap Exploris 480s and a Bruker timsTOF Pro system)
  • high field asymmetric waveform ion mobility (FAIMS Pro) interfaces for posttranslational modification and low input HLA peptide samples
  • triple quadrupole LC-MS/MS systems (Thermo TSQ Quantiva and TSQ Altis)
  • nanoflow HPLC systems for on-line nanoscale chromatography (EASY nLC 1200s, EvoSep Whisper, EASY nLC 1000s, NanoACQUITY, Bruker nanoElute, etc.)

We have a full complement of analytical- to nano-scale liquid chromatography systems for protein and peptide fractionation as well as full suite of conventional protein biochemistry, lipid, and small molecule laboratory apparatus. We have dedicated tissue culture facilities for growing cells for biological validation experiments and quantitative studies via SILAC metabolic profiling and full BL2 capabilities for biological and clinical sample preparation. 

For automation of sample preparation, we have three Agilent Bravo liquid handling robots (two with AssayMap heads for microchromatography-assisted sample preparation), two Thermo KingFisher Flex robots for magnetic bead handling, and a Perkin Elmer Janus Automated Workstation. 

To support data analysis for a wide range of discovery projects in the proteomics platform Spectrum Mill is installed and currently run on three virtual servers each running Windows 2016 Server virtualized via VMware. Each server is configured with 16 or 24 processors, 48 or 56 GB RAM, and 1 TB of storage. MaxQuant is similarly installed and can run on up to eight dynamically instantiated virtual servers with two CPUs and 8 GB RAM each. Bruker timsTOF raw data is processed using PEAKS and MSFragger on a dedicated Windows Virtual Machine (VM) with 24 CPUs and 128 GB of RAM. We also have Spectronaut for analysis of DIA data. Capacity can be added by increasing the number of virtual servers or increased CPU, RAM, or storage all of which can be done with a few hours' notice. Raw data from all mass spectrometers is automatically backed up and archived to network-attached storage with current consumption of 126 TB (from years 2004-2020).

To support bioinformatics analysis of resulting proteomics data tables, our group has developed several R Shiny applications, such as the Proteomic Toolset for integrative analysis (Protigy). These Shiny apps are hosted on an instance of Shiny Server Professional running on a Linux VM with four CPUs and 12 GB of RAM.Publicly accessible Shiny apps developed at the Proteomics platform are hosted on a separate Linux VM (two CPUs, 4 GB RAM) exposed to the world wide web.

The Proteomics group (approx. 35 scientists) consists of postdoctoral associates, highly experienced Ph.D. or Ph.D.-equivalent scientists and technical staff. The Ph.D. group members have expertise spanning biology, clinical medicine, chromatography, instrumentation, and computational analysis. The technical staff consists largely of recent college graduates who train and stay for a period of two to three years before pursuing advanced degrees. In addition, the group has two seasoned administrative personnel that handle grants and collaborative interactions with the greater Broad community of over 1,500 scientists.