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 Merkin building at 415 Main Street, 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, , multiple Orbitrap Exploris 480s, Bruker timsTOF HT and timsTOF SCP systems)
• high field asymmetric waveform ion mobility (FAIMS Pro) interfaces for posttranslational modification and low input HLA peptide samples
• triple quadrupole LC-MS/MS system (Thermo TSQ Altis)
• nanoflow HPLC systems for on-line nanoscale chromatography (Vanquish Neo UHPLC systems, EASY nLC 1200s, Evosep One with Whisper mode, NanoACQUITY, Bruker nanoElute)

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 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 several Agilent Bravo liquid handling robots with AssayMap heads for microchromatography-assisted sample preparation, a Thermo KingFisher Flex robot for magnetic bead handling, an OpenTrons OT-2 Liquid Handler and a Tecan A200 automated SPE manifold.

To support data analysis for a wide range of discovery projects in the proteomics platform, Spectrum Mill is installed and run on four 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. In addition, raw data analysis pipelines—including FragPipe and DIA-NN—are available as cloud-based workflows which can be easily run on arbitrarily large virtual machines using the Google Cloud Platform-based Terra infrastructure. 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, our group has developed several R Shiny and other applications, including the Proteomic Toolset for integrative analysis (Protigy). These Shiny apps are hosted on an instance of the Posit (RStuido) Connect Server running on a Linux VM with eight CPUs and 32 GB of RAM. Publicly accessible Shiny apps developed at the Proteomics platform are also hosted on the VM accessible via the world wide web. To enable flexible, automated and reproducible analysis of complex proteogenomic data, our group has developed PANOPLY, a cloud-based platform implementing a wide array of algorithms tailored for the analysis of proteogenomic data, with extensive applications to cancer. PANOPLY runs on Terra and harnesses cloud-based computing to full advantage. The group also has computational scientists with a strong background in statistics, machine learning, computer science and data analysis for implementing customized software and analysis approaches for specific projects.

The Proteomics group (approx. 35 scientists) consists of postdoctoral associates, highly experienced Ph.D. or Ph.D.-equivalent staff 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.