Researchers have discovered over 1,000 previously unidentified proteins in common samples of metabolites that persist even after attempts to remove them through extraction methods. These results offer new perspectives and strategies for enhancing future metabolomics studies, including a unique protocol for eliminating these proteins during the extraction process. While the study does not discredit past findings, it emphasizes the necessity of proper controls and validation in experimental setups and analysis.
“Scientific progress often arises from a mix of chance and attentive observation. In this instance, we encountered an unusual outcome during an experiment, investigated further, and uncovered this extensive array of proteins that were evading standard metabolite extractions,” explained Dr. Ryan Sheldon, the director of VAI’s Mass Spectrometry Core and the lead author of the study. “These proteins have the potential to mask results and potentially introduce false conclusions. Our hope is that our discoveries will bring attention to these hidden proteins and fortify the field of metabolomics.”
Traditionally, it was believed that the chemicals used in metabolite extraction would eliminate any proteins in the samples, preventing them from affecting the final analysis. However, this study demonstrates that certain proteins persist, which could alter the intended characteristics of the sample and impact the results.
To exclude these potentially troublesome proteins, Sheldon and his team incorporated a filtration step into their standard extraction process that eliminates proteins larger than 3 kilodaltons, encompassing the majority of proteins.
“Ultimately, even with the most advanced instrumentation available, sample preparation issues can hinder the technology’s effectiveness,” Sheldon noted. “Ensuring that our samples are devoid of any interfering proteins is crucial for obtaining precise results. Our findings aid in achieving this goal.”
The study was led by Dr. Molly Hopper, a research scientist at VAI Mass Spectrometry Core, along with former Van Andel Institute Graduate School student, Dr. Rae House, who is now a postdoctoral fellow supported by the Cancer Epigenetics Training Program under Dr. Evan Lien at VAI. Other contributors to the study include researchers from Van Andel Institute, such as Dr. Michael P. Vincent, Dr. Emily Wolfrum, Dr. Christine N. Isaguirre, and others.
