Proteomics

The Proteomics team comprises a highly trained group of technical experts and collaborative partners for research efforts that investigate large-scale sets of proteins or metabolites from cells or tissues.

Research Services 

The Proteomics Center provides mass spectrometry-based multi-omics approaches to support a variety of research projects at the Institute and for external collaborators. The analysis pipelines are mostly centered around proteomics, which is loosely defined as the systematic, large-scale, and high-throughput detection, identification, and quantitation of the protein content of a sample, as well as proteins’ post-translational modifications and the interaction networks they participate in.

In recent years, the team has expanded their capabilities into other omics areas. For example, they have adapted a method in the field of epitranscriptomics to quantify global levels of RNA modifications through the targeted detection of modified ribonucleosides and their isomers. Recently, they have also deployed a pipeline for the detection, identification, and quantitation of the classes of metabolites that are amenable to be characterized by liquid chromatography-based separations coupled to mass spectrometry.

By providing training (or service) in various biochemistry techniques for sample preparation, ranging from whole cell extraction of proteins, peptides, RNAs, or metabolites, to affinity purifications or size exclusion chromatography, the Proteomics team is dedicated to making these technologies accessible to all Stowers labs.

Technology 

LC/MS Systems:
Our main technology platform consists of nanoflow microcapillary liquid chromatography (LC) coupled to electrospray tandem mass spectrometry (MS).

  • 5x | Thermo Scientific LTQ Linear Ion Trap | Custom-made nano-electrospray ionization source (Nano-ESI) | Agilent 1100 Quaternary HPLC
  • 3x | Thermo Scientific Velos-Orbitrap | Nano-ESI | Agilent 1260 Quaternary HPLC
  • 1x | Q-Exactive + | Nanospray Flex Ion Source (Thermo Scientific) | Dionex UltiMate 3000 RSCLnano System | Variable Wavelength Detector (VWD)
  • 1x | Orbitrap Fusion Lumos (Thermo Scientific) | FAIMS Pro (high-Field Asymmetric waveform Ion Mobility Spectrometry) | Nanospray Flex Ion Source | Dionex UltiMate 3000 RSCLnano System | VWD
  • 1x | Orbitrap Eclipse (Thermo Scientific) | FAIMS | Nanospray Flex Ion Source | Dionex UltiMate 3000 RSCLnano
Team Contact 
Laurence Florens, PhD
Head, Proteomics

Laurence Florens established the Proteomics Center at the Stowers Institute in July 2003 with Mike Washburn. Ever since, Florens has developed, adopted, and applied advanced mass spectrometry-based approaches to drive biological discovery in a wide array of collaborative projects, leading to over 240 peer-reviewed publications with 46 different labs.

A native of France, Florens graduated from Nice University with a bachelor’s degree in biochemistry. She received her masters and her doctorate in structural biology and microbiology from Aix-Marseilles I University before completing a postdoctoral fellowship in bioenergetics at Michigan State University. After a short stint at the University of Washington in Seattle, Florens joined the lab of John R. Yates, at The Scripps Research Institute, where she applied proteomics to the malaria parasite. While at the Stowers Institute, she has continued working on apicomplexan parasites’ proteomes via NIH-supported collaborations.

Florens is the 2006 co-recipient of the Hudson Prize from the M.R. and Evelyn Hudson Foundation and a member of the American Society for Mass Spectrometry, the Association of Biomolecular Resource Facilities, the American Chemical Society, and the Human Proteome Organization. She has been a faculty at the Graduate School of the Stowers Institute since its inception and serves on the Editorial Advisory Board for the Journal of Proteome Research.

Featured Publications 
Bhattacharya S, Levy MJ, Zhang N, Li H, Florens L, Washburn MP, Workman JL. Nat Commun. 2020;12:1443. doi: 1410.1038/s41467-41021-21663-w.
Singh NP, De Kumar B, Paulson A, Parrish ME, Scott C, Zhang Y, Florens L, Krumlauf R. [published ahead of print March 4 2021]. Dev Biol. 2021;9.
Liu X, Zhang Y, Wen Z, Hao Y, Banks CAS, Lange JJ, Slaughter BD, Unruh JR, Florens L, Abmayr SM, Workman JL, Washburn MP. Proc Natl Acad Sci U S A. 2020;117:31861-31870.
Tao F, Soffers J, Hu D, Chen S, Gao X, Zhang Y, Zhao C, Smith SE, Unruh JR, Zhang D, Tsuchiya D, Venkatraman A, Zhao M, Li Z, Qian P, Parmely T, He XC, Washburn M, Florens L, Perry JM, Zeitlinger J, Workman J, Li L. Stem Cell Reports. 2020 Sep 8;15(3):662-676. doi: 10.1016/j.stemcr.2020.07.018.
Takahashi H, Ranjan A, Chen S, Suzuki H, Shibata M, Hirose T, Hirose H, Sasaki K, Abe R, Chen K, He Y, Zhang Y, Takigawa I, Tsukiyama T, Watanabe M, Fujii S, Iida M, Yamamoto J, Yamaguchi Y, Suzuki Y, Matsumoto M, Nakayama KI, Washburn MP, Saraf A, Florens L, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Hatakeyama S. Nat Commun. 2020;11:1063. doi: 10.1038/s41467-020-14849-1.
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