ken.hamill@sciex.com

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!

References

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

Why SCIEX partners with experts around the world

Innovation in mass spectrometry does not happen in isolation. Some of the most impactful scientific advances emerge from highly specialized research communities – proteomics experts developing new peptide identification workflows, metabolomics researchers curating spectral databases, toxicologists building compound libraries, and biopharma scientists creating novel characterization methods.

Managing ADC characterization: The challenge of turning complexity into confidence

Unlike traditional monoclonal antibodies, ADCs combine an antibody backbone with linker chemistry and a cytotoxic payload. This multi-component architecture introduces overlapping layers of heterogeneity, including drug-to-antibody ratio (DAR) distributions, charge variants, post-translational modifications, and structural changes at both the intact and subunit levels. Across ADC development, these characteristics are considered critical quality attributes that must be characterized, understood, and monitored.

3 reasons ZT Scan DIA is changing the game in metabolomics

For years, metabolomics researchers have faced a frustrating reality: modern high-resolution mass spectrometers can detect tens of thousands of molecular features, yet only a fraction can be confidently identified. The challenge is no longer finding molecules. It is generating the high-quality MS/MS data needed to confidently assign structures and extract meaningful biological insights.

Posted by

0 Comments