Nav: Home

Researchers can count on improved proteomics method

June 14, 2018

Every cell in the body contains thousands of different protein molecules and they can change this composition whenever they are induced to perform a particular task or convert into a different cell type. Understanding how cells function depends on proteomics, the ability to measure all of the changes in a cell's protein components.

In a recent paper published in the journal Analytical Chemistry, Martin Wühr and colleagues in Princeton University's Department of Molecular Biology described an improved method to accurately count the proteins present in a cell under different circumstances.

The basic tool for counting proteins is a machine called a mass spectrometer. Cell samples can be run through this type of instrument one at a time, but this is laborious and it can be difficult to detect any changes between different samples. An alternative approach is to label all of the proteins in a particular sample with a unique "isobaric" tag. Multiple samples--up to 11--can then be mixed together and run through the mass spectrometer at the same time, with the isobaric tag functioning as an identifying barcode that tells the researcher which sample the protein originally came from. This speeds things up and makes it easier to quantify any changes in the protein composition of different samples.

"However, with the simplest version of isobaric tagging, known as TMT-MS2, there are major difficulties in distinguishing real signals from background noise," Wühr explains. "That makes the readouts unreliable and only semi-quantitative."

A more complex version of isobaric tagging, called TMT-MS3, can improve this signal-to-noise problem, but it is slower and less sensitive. Moreover, it relies on a much more expensive type of mass spectrometer beyond the reach of most researchers.

While he was a postdoc at Harvard University, Wühr developed a different approach to isobaric tagging that solved the signal-to-noise problem while remaining compatible with cheaper, widely available mass spectrometers. But the technique--known as TMTc--was not without its own problems, particularly a lack of precision that made it hard to obtain consistent results.

In their recent Analytical Chemistry paper, Wühr and two of his graduate students, Matthew Sonnett and Eyan Yeung, described an improved version of TMTc that they named TMTc+. By changing how the cell samples are prepared and altering the computer algorithm that extracts data from the mass spectrometer, Wühr and colleagues were able to address many of the limitations associated with the various methods of isobaric tagging.

"The TMTc+ method is in a kind of sweet spot compared to the other methods," Wühr says. "It provides superb measurement accuracy and precision, it's at least as sensitive as any other method, and it's compatible with around ten times more mass spectrometers than TMT-MS3."

Naturally, Wühr says, there is still room for improvement. TMTc+ only allows a maximum of 5 samples to be run at the same time, and the detection of proteins in these samples is relatively inefficient. Both of these problems can be solved by developing new types of isobaric tags. "We have to explore the chemical space of these tags and find ones that work really well," Wühr says. "To this end, we have started a collaboration with the Carell group, organic chemistry experts at the LMU Munich, and already published a proof of principle paper. Eventually, these efforts should lead to an approach that will allow researchers to count every protein in a cell as it changes its form and function."
-end-
M. Sonnett, E. Yeung, and M. Wühr. Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster. Analytical Chemistry. 90(8): 5032-5039. (2018). doi: 10.1021/acs.analchem.7b04713

M. Stadlmeier, J. Bogena, M. Wallner, M. Wühr, and T. Carell. A Sulfoxide?Based Isobaric Labelling Reagent for Accurate Quantitative Mass Spectrometry. Angewandte Chemie International Edition. 57(11):2958-2962. (2018). doi: 10.1002/anie.201708867

Princeton University

Related Proteins Articles:

Discovering, counting, cataloguing proteins
Scientists describe a well-defined mitochondrial proteome in baker's yeast.
Interrogating proteins
Scientists from the University of Bristol have designed a new protein structure, and are using it to understand how protein structures are stabilized.
Ancient proteins studied in detail
How did protein interactions arise and how have they developed?
What can we learn from dinosaur proteins?
Researchers recently confirmed it is possible to extract proteins from 80-million-year-old dinosaur bones.
Relocation of proteins with a new nanobody tool
Researchers at the Biozentrum of the University of Basel have developed a new method by which proteins can be transported to a new location in a cell.
Proteins that can take the heat
Ancient proteins may offer clues on how to engineer proteins that can withstand the high temperatures required in industrial applications, according to new research published in the Proceedings of the National Academy of Sciences.
Designer proteins fold DNA
Florian Praetorius and Professor Hendrik Dietz of the Technical University of Munich have developed a new method that can be used to construct custom hybrid structures using DNA and proteins.
The proteins that domesticated our genomes
EPFL scientists have carried out a genomic and evolutionary study of a large and enigmatic family of human proteins, to demonstrate that it is responsible for harnessing the millions of transposable elements in the human genome.
Rare proteins collapse earlier
Some organisms are able to survive in hot springs, while others can only live at mild temperatures because their proteins aren't able to withstand such extreme heat.
How proteins reshape cell membranes
Small 'bubbles' frequently form on membranes of cells and are taken up into their interior.

Related Proteins Reading:

Proteins: Structure and Function
by David Whitford (Author)

Proteins: Concepts in Biochemistry
by Paulo Almeida (Author)

The High-Protein Vegan Cookbook: 125+ Hearty Plant-Based Recipes
by Ginny Kay McMeans (Author)

Protein Power: The High-Protein/Low Carbohydrate Way to Lose Weight, Feel Fit, and Boost Your Health-in Just Weeks!
by Michael R. Eades (Author), Mary Dan Eades (Author)

How Proteins Work
by Mike Williamson (Author)

The High-Protein Vegetarian Cookbook: Hearty Dishes that Even Carnivores Will Love
by Katie Parker (Author), Kristen Smith (Author)

Structure And Mechanism In Protein Science: A Guide To Enzyme Catalysis And Protein Folding (Series in Structural Biology)
by Alan R Fersht (Author)

Protein Sparing Modified Fast Cookbook
by Maria Emmerich (Author), Craig Emmerich (Author)

DIY Protein Bars Cookbook [3rd Edition]: Easy, Healthy, Homemade No-Bake Treats That Are Packed With Protein!
by Jessica Stier (Author)

The Protein Power Lifeplan
by Michael R. Eades (Author), Mary Dan Eades (Author)

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Approaching With Kindness
We often forget to say the words "thank you." But can those two words change how you — and those around you — look at the world? This hour, TED speakers on the power of gratitude and appreciation. Guests include author AJ Jacobs, author and former baseball player Mike Robbins, Dr. Laura Trice, Professor of Management Christine Porath, and former Danish politician Özlem Cekic.
Now Playing: Science for the People

#509 Anisogamy: The Beginning of Male and Female
This week we discuss how the sperm and egg came to be, and how a difference of reproductive interest has led to sexual conflict in bed bugs. We'll be speaking with Dr. Geoff Parker, an evolutionary biologist credited with developing a theory to explain the evolution of two sexes, about anisogamy, sexual reproduction through the fusion of two different gametes: the egg and the sperm. Then we'll speak with Dr. Roberto Pereira, research scientist in urban entomology at the University of Florida, about traumatic insemination in bed bugs.