​Caj Neubauer

Research Faculty
University of Colorado Boulder
​
​​​​Research interest  |  Ongoing projects  |  
​Publications  |  CV  |  Resources
RESEARCH INTEREST

The frontiers of metabolomics & proteomics are finally merging with isotope ratio mass spectrometry, opening exciting new opportunities in our understanding of biological systems.

My lab at the University of Colorado Boulder helps pioneer related novel molecular measurements based on soft-ionization isotope ratio mass spectrometry. These advances can be used to study natural stable isotope fingerprints in metabolites, drugs, or small inorganic ions for a fascinating range of cross-disciplinary applications in life and earth sciences.

To achieve our longterm goal of making natural isotope patterns universally useful, we combine expertise in metabolomics and proteomics with advanced concepts of high precision stable isotope analysis from geochemistry. If you are interesting in teaming up to develop this new science at the interface of biology, chemistry and  geology, please get in touch. 
ONGOING PROJECTS

​​- Earth & environmental science: isotopocules of oxyanions

- Life sciences: Dietary and metabolic signatures in amino acids & proteins

- Technology & method development for ESI-Orbitrap IRMS

Resources
​
The IsoX software (Isotopolog data eXtraction from Orbitrap RAW files) has now been commercialized by Thermo Fisher Scientific. A demo version is freely available from the company upon request (see Kantnerová  et al. for details).

IsoXL (Isotopologs to eXceL) is a web based interface to process and analyze data from IsoX. It is based on the open-source isoorbi R package that we have programmed. See also our additional isotopocule apps. 

Consider joining the Isoorbi Slack workspace to participate in community discussions and hear about our monthly Zoom meetings.
PUBLICATIONS
  1. Kantnerová K, Kuhlbusch N, Juchelka D, Hilkert A, Kopf SH, Neubauer C (2024) A guide to precise measurements of isotope abundance by ESI-Orbitrap MS. Nature Protocols [LINK]
  2. Neubauer C, Kantnerová K, Lamothe A, Savarino J, Hilkert A, Juchelka D, Hinrichs KU, Elvert M, Heuer V, Elsner M, Bakkour R, Julien M, Öztoprak M, Schouten S, Hattori S, Dittmar T (2023) Discovering nature’s fingerprints: Isotope ratio analysis on bioanalytical mass spectrometers. JASMS [LINK]
  3. Boettger JD, Neubauer C, Kopf SH, Kubicki JD (2022) Microbial denitrification: Active site and reaction path models predict new isotopic fingerprints. ACS Earth and Space Chemistry [LINK]
  4. Coffinet S, Mühlena L, Lipp JS, Weil M, Neubauer C, Urich T,  Hinrichs KU (2022) Evidence for enzymatic backbone methylation of the main membrane lipids in the archaeon Methanomassiliicoccus luminyensis. Applied and Environmental Microbiology [Link]
  5. Neubauer C, Landecker H (2021) A planetary health perspective on synthetic methionine: Implications of opening the tap on a historically limiting nutrient. Lancet Planetary Health [Link]
  6. Hilkert A, Böhlke JK, Mroczkowski SJ, Fort KL, Aizikov K, Wang XT, Kopf SH, Neubauer C (2021) Exploring the potential of Electrospray-Orbitrap for stable isotope analysis using nitrate as a model. Analytical Chemistry [Link]​
  7. Neubauer C,  Cremiere A,  Wang XT,  Thiagarajan N, Sessions AL,  Adkins JF,  Dalleska NF,  Turchyn AV,  Clegg JA,  Moradian A,  Sweredoski MJ,  Garbis SD,  Eiler JM (2020) Stable isotope analysis of intact oxyanions using electrospray Orbitrap mass spectrometry. Analytical Chemistry [Link]
  8. ​Neubauer C, Sweredoski MJ, Moradian A, Newman DK, Robins RJ, Eiler JM (2018). Scanning the isotopic structure of molecules by tandem mass spectrometry. Int J Mass Spec [Link]
  9. Neubauer C, Kasi AS, Grahl N, Sessions AL, Kopf  SH, Kato R, Hogan DA, Newman DK (2018). Refining the application of microbial lipids as tracers of Staphylococcus aureus growth rates in cystic fibrosis sputum. J Bacteriology [Link]  [Commentary]
  10. Neubauer C, Sessions AL, Booth IR, Bowen BP, Kopf SH, Newman DK, Dalleska NF (2018). Towards measuring growth rates of pathogens during infections by D2O-labeling lipidomics. Rapid Communications in Mass Spectrometry [Link]
  11. Newman DK, Neubauer C, Ricci JN, Wu C-H, Pearson A (2016). Cellular and molecular biological approaches to interpreting ancient biomarkers. Annu Rev Earth Planet Sci [Link]
  12. Neubauer C, Dalleska NF, Cowley ES, Shikuma NJ, Wu C-H, Sessions AL, Newman DK (2015). Lipid remodeling in Rhodopseudomonas palustris TIE-1 upon loss of hopanoids and hopanoid methylation. Geobiology [Link]
  13. Voorhees RM, Mandal D, Neubauer C, Köhrer C, RajBhandary UL, Ramakrishnan V (2013). The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome. Nat Struct Mol Biol [Link]
  14. Neubauer C, Gillet R, Kelley AC, Ramakrishnan V (2012). Decoding in the absence of a codon by tmRNA and SmpB in the ribosome. Science [Link]
  15. Neubauer C, Gao Y-G, Andersen KR, Dunham CM, Kelley AC, Hentschel J, Gerdes K, Ramakrishnan V, Brodersen DE (2009). The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Cell [Link]
  16. Weixlbaumer A, Jin H, Neubauer C, Voorhees RM, Petry S, Kelley AC, Ramakrishnan V (2008). Insights into translational termination from the structure of RF2 bound to the ribosome. Science [Link]
  17. Klages J, Neubauer C, Coles M, Kessler H, Luy B (2005). Structure Refinement of Cyclosporin A in chloroform by using RDCs measured in a stretched PDMS-gel. Chembiochem [Link]

PATENTS
  1. Eiler JM, ​Neubauer SC​, Sweredoski MJ, Griep-Raming J (Issued: 2023; Filed: 2019). Isotopic mass spectrometer. ​United States Patent No. US 11,626,275 B2  [Link] 

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