A region-resolved proteomic map of the human brain enabled by high-throughput proteomics

Presentation from our Virtual User and Applications Meeting

Overview

The study introduces a high-throughput microflow liquid chromatography mass spectrometry (LC–MS) setup, specifically using the timsTOF HT platform equipped with VIP HESI, a vacuum insulated probe heated electrospray ionization source. Johanna Tüshaus et al., established the workflow and created a protein expression map of 13 distinct brain regions, encompassing over 11,000 proteins. This resource uncovers brain region-enriched protein expression patterns, functional protein classes, and differences in protein localization among brain regions. A dedicated R Shiny app facilitates data exploration. Key findings include the scalability, robustness, and sensitivity of the microflow LC–MS approach and identification of unique proteomic fingerprints for each brain region.

Key Learnings:

  • High-Throughput Microflow LC–MS Setup: Utilizing the timsTOF HT platform with VIP HESI offers enhanced throughput and robustness compared to traditional nanoflow setups.
  • Scalability and Sensitivity: The microflow LC–MS system allows for deep proteomic analysis with minimal sample requirements, outperforming traditional methods while mastering the highest level of robustness, analyzing more than 2,000 consecutive samples prepared from formalin-fixed paraffin embedded (FFPE) material.
  • Efficient FFPE Protein Extraction: The study establishes an efficient protocol for extracting quantitative protein expression data from FFPE material.
  • Identification of Unique Proteomic Fingerprints: Distinctive protein expression patterns for each brain region are uncovered, facilitated by the capabilities and robustness of the microflow LC–MS setup.

Speaker

 

"Planning a large-scale proteomic profiling project, we were in need of a fast, sensitive and robust LC-MS/MS setup. Coupling our well-established micro-flow LC technology via the VIP-HESI source to the timsTOF HT turned out to be a powerful combination. It enables deep proteome coverage using short gradients thereby linking speed with sensitivity. The development of the 50 µm ESI emitter was key to boost the sensitivity of our micro-flow LC timsTOF setup."

Johanna Tueshaus, Ph.D., Postdoctoral researcher, Technical University Munich, Germany

 

For Research Use Only. Not for use in clinical diagnostic procedures.