The 2020 PRG Beer Proteomics Study
If – like me – you have spent a large portion of this pandemic watching the television show Friends, you might be familiar with the episode where Ross and Mike try to determine the differences between beer and lager.
Their experiment is somewhat futile, yielding little to no results nor firm scientific conclusions. Of course, it is fictitious, but the notion of understanding the molecular composition of alcoholic beverages is very much real. Scientists at the ABRF Proteomics Research Group (PRG) are exploring the protein composition of different types of beer using a mass spectrometry-based approach. Formally titled Processing and analyzing a mixed, fermented yeast-plant proteome (or, The 2020 PRG Beer Proteomics Study), the project is recruiting research groups across the world.
What is the proteome?
A proteome is the complete set of proteins that is expressed in an organism, whether it be at the cellular level or in a specific type of tissue, at a specific time.
The brief is fairly straightforward. First, drink beer (this does not have to be alcoholic). Second, take a sample of the beer, digest the proteins, analyze the sample using mass spectrometry and report the protein information that is discovered. The PRG are collecting the raw data and evaluating the unique or dissimilar qualities of samples.
The project was born, ironically, over a few beers. "I think the idea started while we were drinking beer, maybe more as a joke, and then the more we thought about it, it was actually a really good idea. When the rest of the PRG heard about it, they liked it, and one thing led to another," said Benjamin Neely, co-chair of the PRG and research chemist at the National Institute of Standards and Technology.
The allure of an arguably unconventional sample drew in Brett Phinney, member of the PRG and manager of the proteomics core at the University of California (UC) Davis. The university has a strong reputation for beer brewing, and the first phase of project participants received an aliquot of The PRG Pale Ale that was brewed by Glen Fox. "Our partners at UC Davis Brewing brewed a special control beer (which is delicious, by the way) that we can use as a control across laboratories. We sent that out to over 60 laboratories all over the world," said Phinney.
A helping hand for metaproteomics
When asked about the potential applications of this study for the beer industry, Phinney replied, "For me this is essentially basic research. What proteins can we detect in beer, are there any major differences we can detect? Can we make sense out of data from different laboratories from around the world? I do hope others will be able to make use out of the data perhaps down the road, but we will see."
However, the amount of data collected from different research groups that are analyzing different samples will be useful for benchmarking bioinformatic workflows. Neely explained, "Normally when we perform proteomic analysis, we are just focused on one species, say a human. But there are many sample types of mixed species, like sediment, corals or beer." This approach to proteomics research is known as metaproteomics (also referred to as community proteomics).
"When analyzing beer you are looking at the proteome of yeast, plants (wheat, rice, hops and more), and sometimes bacteria depending on the brew. Some of these are known, while some are unknown (like the bacteria added to a sour)," Neely added.
How to analyze data from different species that includes known and unknown proteins is as a prevalent challenge in metaproteomics. The PRG team hope that making the data from the study public will be useful for the field in general: "Since all the data we generate for this study will be made public, we expect it to be useful to check and compare metaproteomic workflows to identify unknown species, but also to see how different workflows predict functional changes occurring in known species present. But most importantly, it will be a data set that is fun to look at because of its relevance," Neely said. He added that "There are some really great bioinformaticians out there who will enjoy the data and its inherent complexity."
A pint-sized project
Aside from generating unique and interesting data, the study is also a community-building exercise that will enable the PRG to be productive whilst the group conduct internal testing for its next large study.
Unsurprisingly, the pandemic poses logistical challenges for the team. Lockdowns and social distancing measures are making it hard to find laboratory time, and the PRG group all work on other projects in areas such as COVID and cancer research. "I’m usually selfish when I help design experiments. I say, 'How can I rope people in with helping us with the science we want to accomplish and make new friends/colleagues in our little niche proteomics community?' These studies are great for doing both," said Phinney.
A logistical challenge that was perhaps more surprising was shipping the control samples. It turns out that a group of scientists shipping 1 ml aliquots of home brew across the world triggers a few questions from the customs department; questions that were – thankfully – answered.
In spite of these difficulties, the PRG team continue to pursue the study and anticipate that the next hurdle will be data analysis: "It will be challenging to try and make any sense out of this data seeing as it comes from a wide variety of laboratories using different methods," said Phinney. The control brew will be an asset here.
"Once people generate the data, we think that we can use some ID-free approaches to generate some high-level comparisons (like clustering across beer types and region). Our primary goal will be to turn around and provide the data back to the community," Neely added.
The data is due at the end of January, and the scientists hope to present some preliminary results in March. The deadline to receive the PRG control beer has passed, but you can still sign up to the study and use the commercial beer, Heineken, as a control.
Benjamin Neely and Brett Phinney were speaking to Molly Campbell, Science Writer, Technology Networks.
The 2020 PRG Beery Proteomics study is funded by the ABRF. The control sample was donated, and the time/effort of PRG members and study participants is voluntary.