Industrialize Your Quantitative Proteomics Using a More Simplified Sample Prep

May 24, 2016 | Blogs | 0 comments


Robust, Reproducible, Sample Preparation

Part 3 of a 3-Part Blog Series

In part 1 and part 2 of this blog series we discussed how you can increase your efficiency for high throughput quantitative proteomics by industrializing your sample analysis and data processing. Microflow SWATH® Acquisition on your TripleTOF® system coupled with OneOmics™ data analysis tools allow you to run samples faster, collect data faster, and process your data files faster. It all adds up to getting more meaningful biological information in a shorter amount of time.

Except there’s still one problem. Your sample preparation is now the bottleneck. Your time is too valuable to waste on repetitive pipetting. It’s time to revolutionize your sample preparation and industrialize your entire workflow! Whether you’re working with biological fluids, cell lines, or tissues, there are automated strategies that can alleviate the time-sink of manual sample preparation.

Researchers from SCIEX, Cedars Sinai Medical Center, and Beckman Coulter demonstrate the advantages of using a Biomek NXP Span-8 Workstation and Protein Preparation Kits with ready-to-use reagents and methods to automate protein digestion of biofluids. The Biomek workstation puts every aspect of liquid handling – including pipetting, dilution, dispensing and integration – into a single, automated system. The all-in-one protein preparation kits provide all the reagents for automated protein denaturation, reduction, alkylation, and trypsin digestion for 96 samples at a time. Besides automating routine tasks and freeing valuable researcher time, they also reduce day-to-day variability resulting from a manual, time-consuming, multi-step protocol.

As demonstrated, very high day-to-day reproducibility within a lab, as well as between different labs, can be obtained. Over 80% of peptides monitored by LC-MS had digestion reproducibility below 10% CVs. And most importantly, similar performance was observed in multiple labs on multiple days1.

The end result – higher reproducibility, higher efficiency, less personal burden for mundane tasks, and more valuable time for other research inquiries.

Learn more about how Dr. Jenny van Eyk and her team are developing robust pipelines for targeted proteomic analysis to do population-scale proteomics by watching her webinar2: Proteome Centric Precision Medicine – Embracing Pathological Diversity.

The Biomek workstation and protein preparation kits are an excellent solution for liquid phase samples, biological fluids, and cell lines. But what if you’re working with tissues or tumors or other complex or challenging biospecimens?

Here’s where the PCT-HD Pressure Cycling Technology High Definition sample preparation system can help. PCT-HD sample preparation enables faster, less cumbersome and higher quality homogenization, extraction and digestion of proteins from tissue samples by utilizing controlled cycles of pressure to break apart the samples. This process results in faster and improved sample processing, and a higher quality of results.

As demonstrated in a recent webinar3, the PCT-HD provides hands-free sample homogenization and integrated disposable tools for up to 16 samples per batch. PCT also helps to digest not only poorly soluble membrane proteins, but also many tightly folded proteins that can resist digestion under conventional conditions. The method takes less than 40 minutes of hands-on operator time and is completed in about 4 hours, including a post-digestion sample clean-up with solid phase extraction columns.

The end result – faster sample preparation for tissue samples that provides even better results than manual preparation.

Learn more about how PCT sample preparation combined with SWATH acquisition can provide high-quality quantitative data for tissue proteomics in this webinar4 by Dr. Tiannan Guo from Professor Ruedi Aebersold group (Institute of Molecular Systems Biology, ETH Zurich).

Finally, maintaining an industrialized quantitation proteomics pipeline also requires quality control and performance benchmarking. SCIEX will soon launch a SWATH Acquisition Performance Kit which provides samples and methods for assessing the status of your LC-MS system, for getting started on running SWATH experiments and for benchmarking the data quality of your SWATH results.

So don’t let sample prep be your rate-limiting step! To learn more about how you can revolutionize and industrialize your sample preparation protocol, read the full technical noteand view the webinars2,3,4. And to see how you can industrialize your entire proteomics workflow to improve your efficiency and save valuable time during sample analysis and data analysis, see part 1 and part 2 of this blog series.


  1. Automating Protein Digestion for Reproducible Proteomics
  2. Proteome Centric Precision Medicine – Embracing Pathological Diversity – Dr Jenny van Eyk, Cedars-Sinai Medical Center
  3. PCT Sample Preparation for SWATH-MS Tissue Proteomics – Dr. Alex LAZAREV, Pressure BioSciences, Inc.
  4. High-Throughput SWATH-MS for Biopsy-Level Samples – Dr. Tiannan Guo, ETH Zurich


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Christie Hunter is the Director of Applications at SCIEX. Christie has worked at SCIEX for 20 years, pioneering many workflows in quantitative proteomics. Christie was an early user of SWATH acquisition and played a big role in evolving the workflows and driving adoption of this new data independent approach with many proteomic researchers. Christie and her team are focused on developing and testing innovative MS workflows to analyze biomolecules, and work collaboratively with the instrument, chemistry and software research groups.


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