Please see the computational and experimental protocols used in our research.


Mass spectrometry

Orbitrap Elite

We have access to the shared mass spectrometry (MS) facilities through collaboration with Drs. Robert Hettich and Gregory Hurst in the Mass Spectrometry and Laser Spectroscopy group of the Chemical Science Division. The available mass spectrometers include an LTQ Orbitrap Elite, an LTQ Orbitrap Velos, and an LTQ Orbitrap XL. Each mass spectrometer is interfaced via electrospray with high-performance liquid chromatography (HPLC) equipments (LC Packings Ultimate HPLC, Switchos flow switching module, or Thermo Finnigan Accela). We use these LC-MS/MS systems to perform shotgun proteomics measurements as described in this protocol.



We have access to an InfiniBand cluster (Viper) and a Panasas file server. The InfiniBand cluster includes ten 64-core compute nodes (each with four 16-core AMD CPUs and 256 GB RAM). The Panasas file server has 62 TB of storage space. We obtain high-performance computing allocations on Titan from Oak Ridge Leadership Computing Facility (OLCF) through user proposals. Titan is a 20+ petaflops Cray XK7 supercomputer with a CPU/GPU hybrid architecture.



We obtain large-scale sequencing allocation from DOE Joint Genome Institute (JGI) through user proposals. Small sequencing projects are completed using commercial sequencing services.