We are proud to be part of a newly published peer-reviewed study in Nature Communications. By combining PASEF-enabled mass spectrometry with de novo protein sequencing, the team greatly improved sensitivity and detection in complex microbiomes. The approach introduces the concept of a "druggable metaproteome", offering a new framework to advance microbiome research and develop therapeutic strategies for Crohn's disease and other intestinal inflammatory diseases.
KITCHENER, Ontario, July 21, 2025 /PRNewswire-PRWeb/ -- We are proud to be part of a newly published peer-reviewed study in Nature Communications, led by Dr. David Gomez-Varela at the University of Vienna/Bruker Center of Excellence for Metaproteomics. The study presents a major advancement in metaproteomics by overcoming longstanding barriers in reference databases and data interpretation through the use of ultra-sensitive mass spectrometry techniques and de novo protein sequencing. Our software was integrated into the core data analysis workflow, enabling the identification of proteins in the so-called "dark metaproteome" — those undetectable by conventional tools.
Metaproteomics enables the direct measurement of protein function from both microbes and host organisms in complex environments, such as soil, ocean water, or the human gut. However, the field has been limited by the inability to detect low-abundance proteins, incomplete reference databases, and underutilized MS/MS spectra. Over 80% of microbial species identified at the genetic level remain unseen at the protein level, a gap referred to as the "dark metaproteome."
To tackle this challenge, the research team developed uMetaP, a powerful integration timsTOF-based liquid chromatography-mass spectrometry (LC-MS) technology and a de novo sequencing strategy, novoMP. The timsTOF platform leverages Parallel Accumulation Serial Fragmentation (PASEF), an innovative method that boosts both speed and sensitivity, particularly in complex samples such as microbiomes. NovoMP, powered by a custom-trained version of the Novor algorithm and trained on over 1.75 million high-quality peptide-spectrum matches, enabled a dramatic expansion in the identification of previously uncharacterized peptides, enhancing both taxonomic resolution and functional insight by up to 5,000-fold.
"Conventional database searching is powerful, but it leaves a vast amount of the acquired mass spectrometry data untouched, especially in complex microbiome samples," said Dr. Bin Ma, Chief Scientist and founder of Rapid Novor, Inc. "de novo sequencing provides an effective approach to unlock that hidden data. This work represents a significant leap in our ability to explore the unknown biology in complex microbial communities."
The study marks the first application of a de novo peptide sequencing algorithm fully optimized for PASEF data, and shows that de novo sequencing can complement and even surpass traditional database searches in certain contexts, particularly where reference sequences are missing or incomplete.
"Having a timsTOF trained version of Novor directly integrated into Bruker's ProteoScape is a game-changer. It brings the power of real-time de novo sequencing directly into our proteomics workflows, enabling us to uncover novel biology that would otherwise remain hidden. Combined with ProteoScape's seamless orchestration of acquisition, analysis, and interpretation, we're accelerating discoveries in ways that were simply not possible before." said Dr. Dennis Trede, Vice President, Software R&D, Life Science Mass Spectrometry, Bruker Daltonics GmbH & Co. KG.
This interdisciplinary collaboration demonstrates the power of combining next-generation hardware, machine learning, and custom algorithms to advance fundamental science and microbial research. Unlocking the dark metaproteome and gaining insight into interactions between the microbiome and the human gut could uncover novel drug targets and open new avenues for treating inflammatory intestinal diseases in humans.
The peer-reviewed paper is available in Nature Communications: Xian et al. Ultra- sensitive metaproteomics redefines the dark metaproteome uncovering host-microbiome interactions and drug targets in intestinal diseases.
* PASEF and timsTOF are trademarks of Bruker Daltonics. All other trademarks are the property of their respective owners.
About Rapid Novor
Rapid Novor Inc., is the world's leader in protein sequencing technology. Specializing in the field of mass spectrometry-based proteomics, the team has developed the technology to directly sequence peptides and proteins without needing access to genomic information. Located at the Kitchener-Waterloo high-tech hub, the company continues to build its technology portfolios based on years of scientific research and inventions. The company's vision is to elevate human health by decoding immunity. For information, please visit http://www.rapidnovor.com. Follow @rapidnovor on X (formerly Twitter) or LinkedIn.
Media Contact
Mingjie Xie, Rapid Novor, Inc., 1 (855) 899-9990, [email protected], rapidnovor.com
SOURCE Rapid Novor, Inc.
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