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The FPDDC operates out of the Proteome Exploration Laboratory (PEL) in Caltech's Beckman Institute. In addition, numerous other Caltech groups and facilities contribute to FPDDC's works. These include:

Bioinformatics Resource Center, Beckman Institute!/

The Caltech Bioinformatics Resource Center (CBRC) develops bioinformatics workflows, facilitates data analysis of biological data, benchmarks methods, provides bioinformatics/statistics consulting, and teaches via training sessions and workshops. The Resource Center supports projects involving both technology development and biological discovery. The current emphasis of this center is bioinformatics for genomics, transcriptomics and epigenomics.

Biological Imaging Facility, Beckman Institute

The mission of the Beckman Institute Biological Imaging Facility (BIF) is to provide state of the art microscopy resources that enable Caltech scientists to conduct the most advanced research possible. The Biological Imaging Facility (BIF, formerly called the Biological Imaging Center, BIC) is the only core facility on the Caltech campus providing light microscopy resources. In addition to its 10 microscopes, the BIF also provides software resources for processing and analyzing image data.

Chou Lab

The primary area of the Chou lab's research focuses on the enzyme p97, also known as the Transitional Endoplasmic Reticulum ATPase (TER). p97/TER uses the energy derived from ATP-hydrolysis to carry out several different cellular functions. It coordinates these functions through association with a myriad of cofactor/adapter proteins. The Chou lab employs a combination of chemical biology, quantitative proteomics, high-throughput, high-content screenings, and biochemical reconstitution to study the mechanism by which p97 orchestrates two major protein clearance pathways, proteasome and autophagy, as well as how it regulates the activity of proteins involved in apoptosis. These processes are especially vital in cancer cells due to an increased reliance on protein clearance of mis-folded proteins, making p97 an attractive cancer target.

Cryo-EM Center, Beckman Institute

The Caltech Cryo-EM Center provides advice, training, and access to high-end instrumentation for Caltech researchers and associates. The resource center is involved in projects in cell biology, structural biology, biochemistry, chemistry, and materials science, including both basic research and technology development.

Millard and Muriel Jacobs Genetics and Genomics Laboratory (MMJGGL)

The Millard and Muriel Jacobs Genetics and Genomics Laboratory provides genomic research tools to Caltech scientists, with an emphasis on high-throughput sequencing and microarray analysis. The Laboratory is equipped with the necessary experimental and bioinformatics infrastructure to generate, store, and analyze large-scale datasets from the Illumina HiSeq2500 high-throughput sequencer and several microarray platforms.

Merkin Institute for Translational Research

The Merkin Institute helps Caltech scientists and engineers transform breakthroughs into advances in human health. Focusing enhanced resources and guidance to mobilize science at points along the translational arc from basic discovery through to clinical collaboration and the introduction of new treatments, the institute facilitates the translation of knowledge into healthcare products and services.

Molecular Observatory, Beckman Institute

The Molecular Observatory provides the Caltech community with advice, training, and access to exceptional capabilities in macromolecular crystallography. The Observatory strives to develop X-ray related methods to meet each user's research objectives and to design experiments to answer hitherto hard to address questions.

Protein Expression Center, Beckman Institute

The Protein Expression Center (PEC) was established to provide researchers with large amounts of proteins of interest to their work. It is equipped for the small, medium, and large-scale cultures of a variety of cells, including bacterial, yeast, insect, and mammalian cell lines. PEC currently specializes in the use of the baculovirus expression system, a widely used and versatile eukaryotic system which has been used to successfully express thousands of proteins. Depending upon the level of expression of a given protein, quantities ranging from hundreds of micrograms to tens of milligrams may be readily produced using resources at the facility. In addition, the Center is also equipped to perform routine molecular biological techniques, including vector construction and PCR analysis of recombinant viruses, as well as purification of expressed recombinant proteins.

Sternberg Lab

The Sternberg laboratory is interested in the systems biology of nematodes, seeking to understand how the properties of an organism – its development, physiology and behavior – are encoded in its genome. The Sternberg Lab primarily uses molecular genetics of the nematode Caenorhabditis elegans but also applies proteomics, computational biology, biochemistry, cell biology, imaging, behavioral analysis, optogenetics, synthetic biology to not only C. elegans but also parasitic nematodes, budding yeast, mice, jellyfish, fungi, and human cells as needed.

X-Ray Crystallography Facility, Beckman Institute

The X-Ray Crystallography Facility (XRCF) has been supporting scientific research at Caltech since 1992. Since inception, our primary mission has been to determine the crystal structures of small molecules, including organic, inorganic and organometallic compounds. The facility provides the appropriate personnel, equipment, and computing facilities for collecting X-ray diffraction data and determining the structures of small molecules from crystalline materials. In addition to small molecule X-ray crystallography (XRC), the facility has expanded to include X-ray powder diffraction (XRPD) and elemental analysis (EA). Details for each technique can be found at the facility website.