ANALYZE

VISUALIZE

CONNECT

DISCOVER

HOW IT WORKS

01

ANALYZE

We can help you prep your skin surface/microbiome, gut microbiome, bacterial cultures, and synthetic biology samples for analysis on our state of the art high resolution mass spectrometers so that the data is discovery ready.

Combined with our computational pipelines, we can help identify and quantify the observed molecules in your samples. 

02

CONNECT

Enrich your analysis by not simply looking at each molecule in isolation, but by connecting it to families of compounds and to all public data containing over 500M molecules. These rich collections can bring context and new hypotheses that guide both understanding and future directions for discovery. 

03

VISUALIZE

Thousands of molecules can measured in a single sample, and with full studies reaching into the millions of data points, rich, interactive, and meaningful visualization are necessary to derive knowledge and understanding. We offer visualization such as molecular molecular, 3D cartography maps, and custom visualizations, to help convey dense experimental data in a natural way. 

 
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ABOUT US

OUR VISION

The hidden chemical signatures around us have a story to tell: where we’ve been, where we are, and where we are going. Ometa Labs’ vision is to empower customers, through a socially data driven infrastructure to measure, connect, visualize, and understand the hidden chemical world. 

OUR TECHNOLOGY

Ometa Labs uses high throughput untargeted tandem mass spectrometry to detect and quantify thousands of molecules in biological samples. We have applied our technology to the skin surface/microbiome, gut microbiome, drug discovery, drug metabolism, forensics, bacterial cultures, synthetic biology, and many more. Combining both proprietary and public databases of mass spectrometry and other omics data and metadata, Ometa Labs’ machine learning algorithms infers the relationship between molecules and the biological and environmental context in which they are found. 

 

OUR TEAM

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MINGXUN WANG PHD

A recently minted Ph.D. from UC San Diego. Ming completed his graduate education with Prof. Nuno Bandeira. His work spanned from proteomics to metabolomics to natural product discovery. Ming has developed algorithms, scaleable analysis platforms, and interactive visualizations. Together with Prof. Pieter Dorrestein and Prof. Nuno Bandeira, Ming helped to establish a new paradigm of collaborative crowd-sourced research in natural products and metabolomics. 

CHRISTOPHER RATH PHD

Scientific leader with 19+ years of experience in discovering innovative analytical solutions in small biotech, big pharma and academia.  His work has explored the interactions of microbes with their environments, in both the infectious disease and synthetic biology spaces. Specific areas of expertise include experimental mass spectrometry, natural products, metabolomics, and large multi -omic experiments.

 
 

Publications

Big Data Algorithms

Alan K. Jarmusch, Mingxun Wang, Christine M. Aceves, Rohit S. Advani, Shaden Aguire, Alexander A. Aksenov, Gajender Aleti et al. Repository-scale Co-and Re-analysis of Tandem Mass Spectrometry Data. bioRxiv (2019): 750471.

Mingxun Wang, Jian Wang, Jeremy Carver, Benjamin S. Pullman, Seong Won Cha, and Nuno Bandeira. "Assembling the community-scale discoverable human proteome." Cell systems 7, no. 4 (2018): 412-421.

Antonio, Gonzalez Jose A. Navas-Molina, Tomasz Kosciolek, Daniel McDonald, Yoshiki Vázquez-Baeza, Gail Ackermann, Jeff DeReus et al. "Qiita: rapid, web-enabled microbiome meta-analysis." Nature methods 15, no. 10 (2018): 796.

Scheubert, Kerstin, Franziska Hufsky, Daniel Petras, Mingxun Wang, Louis-Felix Nothias, Kai Duehrkop, Nuno Bandeira, Pieter C. Dorrestein, and Sebastian Boecker. "Significance estimation for large scale metabolomics annotations by spectral matching." Nature communications 8, no. 1 (2017): 1494.

Bolyen, Evan, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander et al. "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2." Nature biotechnology 37, no. 8 (2019): 852-857.

Mingxun Wang, Alan K. Jarmusch, Fernando Vargas, Alexander A. Aksenov, Julia Gauglitz, Kelly Weldon, Daniel Petras et al. "MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data." bioRxiv (2019): 591016.

Microbiome

Amina Bouslimani*, Carla Porto*, Christopher M. Rath*, Mingxun Wang, Yurong Guo, Antonio Gonzalez, Donna Berg-Lyon, Gail Ackermann, Gitte Julie Moeller Christensen, Teruaki Nakatsuji, Lingjuan Zhang, Andrew W. Borkowski, Michael J. Meehan, Kathleen Dorrestein, Richard L. Gallo, Nuno Bandeira, Rob Knight, Theodore Alexandrov, Pieter C Dorrestein. Molecular cartography of the human skin surface in 3D. Proceedings of the National Academy of Sciences.  (2015) 112(17): E2120-E2129.

Garg, Neha, Mingxun Wang, Embriette Hyde, Ricardo da Silva, Alexey Melnik, Ivan Protsyuk, Amina Bouslimani et al. "Three Dimensional Cartography of Microbiome and Metabolome Data onto Radiological Images of the Human Lung." (2018).

Christopher M. Rath, Theodore Alexandrov, Steven K. Higginbottom, Jiao Song, Marcos E. Milla, Michael A. Fischbach, Justin L. Sonnenburg, Pieter C. Dorrestein. Molecular analysis of model gut microbiotas by imaging mass spectrometry and nanodesorption electrospray ionization reveals dietary metabolite transformations. Analytical Chemistry. (2012) 84:21 9259-9267.

Christopher M. Rath*, Benjamin Janto*, Josh Earl, Azad Ahmed, Fen Z. Hu, Luisa Hiller, Meg Dahlgren, Rachael Kreft, Fengan Yu, Jeremy J. Wolff, Hye Kyong Kweon, Michael A. Christiansen, Kristina Håkansson, Robert M. Williams, Garth D. Ehrlich, and David H. Sherman. Meta-omic characterization of the marine invertebrate microbial consortium that produces the chemotherapeutic natural product ET-743. ACS Chemical Biology. (2011) 6:11, 1244-1256.

Bacterial Metabolomics

William Sawyer, Lisha Wang, Tsuyoshi Uehara, Pramila Tamrakar, Ramadevi Prathapam, Mini Mostafavi, Daryl Richie, Louis Metzger IV, Brian Feng, Christopher M. Rath. Targeted lipopolysaccharide biosynthetic intermediate analysis with normal-phase liquid chromatography mass spectrometry. PLoS one. (2019) 14(2), e0211803. 

Mina Mostafavi, Lisha Wang, Lili Xie, Kenneth T Takeoka, Daryl L Richie, Fergal Casey, Alexey Ruzin, William S Sawyer, Christopher M. Rath, Jun-Rong Wei, Charles R Dean. Interplay of Klebsiella pneumoniae fabZ and lpxC mutations leads to LpxC inhibitor-dependent growth resulting from loss of membrane homeostasis. mSphere. (2018) 3(5), e00508-18.

Christopher M. Rath, Bret M Benton, Javier de Vicente, Joseph E Drumm, Mei Geng, Cindy Li, Robert J Moreau, Xiaoyu Shen, Colin K Skepper, Micah Steffek, Kenneth Takeoka, Lisha Wang, Jun-Rong Wei, Wenjian Xu, Qiong Zhang, Brian Y Feng. Optimization of CoaD inhibitors against Gram-negative organisms through targeted metabolomics. ACS Infectious Diseases. (2017) 4(3), 391-402.

Jun-Rong Wei, Daryl L Richie, Mina Mostafavi, Louis E Metzger, Christopher M Rath, William S Sawyer, Kenneth T Takeoka, Charles R Dean. LpxK is essential for growth of Acinetobacter baumannii ATCC 19606: relationship to toxic accumulation of lipid A pathway intermediates. mSphere. (2017) 2(4) e00199-17.

Dustin Dovala, Christopher M. Rath, Qijun Hu, William S. Sawyer, Steven Shia, Robert Elling, Mark Knapp, Louis E. Metzger IV.  Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism.  Proceedings of the National Academy of Sciences (USA). (2016) 113(41): E6064-E6071.

Daryl L. Richie, Kenneth T. Takeoka, Jade Bojkovic, Louis E. Metzger IV, Christoper M. Rath, William S. Sawyer, Jun-Rong Wei, Charles Dean. Toxic accumulation of LPS pathway intermediates underlies the requirement of LpxH for growth of Acinetobacter baumannii ATCC 19606.  PLoS one. (2016) 11(8): e0160918.

Jade Bojkovic, Daryl L Richie, David A Six, Christopher M. Rath, William S Sawyer, Qijun Hu, Charles R Dean. Characterization of an Acinetobacter baumannii lptD Deletion Strain; Permeability Defects and Response to Inhibition of Lipopolysaccharide and Fatty Acid Biosynthesis. Journal of Bacteriology. (2015) 198(4): 731-741.

Jun-Rong Wei, Daryl L Richie, Mina Mostafavi, Louis E Metzger, Christopher M Rath, William S Sawyer, Kenneth T Takeoka, Charles R Dean. LpxK is essential for growth of Acinetobacter baumannii ATCC 19606: relationship to toxic accumulation of lipid A pathway intermediates. mSphere. (2017) 2(4) e00199-17.

CONTACT US

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Tel: 650-646-4986
3210 Merryfield Row
San Diego, CA 92121