Improved complex sample processing for higher quality of results, reproducibility and depth of proteomic analysis

Jul 28, 2016 | Blogs, Life Science Research, Proteomics | 0 comments


SCIEX partners to improve depth of proteome coverage
SCIEX and Pressure BioSciences address a major challenge for researchers performing complex sample preparation by marketing a complete solution to increase the depth, breadth, and reproducibility of protein extraction, digestion, and quantitation in all tissue types, especially challenging samples like tumors.

How it’s done!
Pressure Cycling Technology (PCT) Sample Preparation Systems utilize controlled cycles of pressure to break apart the tissue samples. Scientists see faster and improved sample processing, and a higher quality of results. When combined with SWATH® Acquisition, high quality protein quantitation results can be obtained on 1000s of proteins in 100s of samples. Thus, combining SWATH® Acquisition with PCT sample preparation makes reproducible proteome research feasible across the enormous diversity of complex biological samples.

Who developed it and Why?
PCT-HD was developed by PBI scientists and engineers in collaboration with Professor Ruedi Aebersold and Dr. Tiannan Guo at ETH Zurich. Drs. Aebersold and Guo combined PCT-HD sample preparation with SCIEX’s SWATH Mass Spectrometry in an effort to standardize the protocol for reproducible, comprehensive quantitation from complex samples. This unique protocol is capable of processing up to 16 samples in six hours1, much faster than current methods.

“By addressing the significant challenges inherent in complex sample preparation to reproducibly analyze thousands of proteins in hundreds of samples, PCT-SWATH accelerates proteomics research in biologically and clinically relevant contexts,” states Dr. Aebersold. “This should increase the productivity of biomarker research, potentially leading to significant improvements in healthcare, including personalized medicine.

Why PCT-HD with SWATH®Acquisition?

  • Simplified handling of small tissue samples
  • Hands-free sample homogenization, integrated disposable tools
  • Simultaneous batch-processing of up to 16 samples
  • Significantly reduced sample preparation time
  • Greater reproducibility of protein quantitation
  • More comprehensive datasets across large sample numbers
  • PCT sample preparation combined with SWATH data acquisition provides a robust quantitative solution for tissue proteomics

The Goal and Solution
Our goal is to industrialize proteomics by enabling efficient, reproducible and automated workflows specifically targeting analysis of small tissue samples for life science research. As the promise of precision medicine research continues to evolve, researchers will need powerful tools and application support to perform the Omics research that creates the scientific foundation of precision medicine. This solution from SCIEX and PBI is expected to significantly expand the footprint of MS-based quantitation workflows in clinical research settings worldwide.

Most recently, the Aebersold lab has combined the latest PCT technology with SWATH® acquisition to achieve a 40% increase in peptide quantitation over traditional methods.1 This means deeper proteome coverage with less sample input requirements.

To learn more about how the PCT sample prep workflow, our partners at PBI have recorded a short video.

Want to know more about available methods? Comment below!


  1. Shao S, Guo T, Gross T, Lazarev A, Koh CC, Joerger M, Jochum W, Aebersold R. 2016 J Proteome Research. 15(6): 1821-9.


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