Caj Neubauer

Natural Scientist
Boulder, Colorado
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​​​​Research interests  |  Ongoing projects  |  
​Publications  |  CV  |  IsoX | IsoXL  |  Isotopocule apps
RESEARCH INTERESTS

My research is focused on two small molecules that shape the Earth system and whose roles are profoundly changing due to human activity.  Nitrate  – the chemical form in which plants assimilate nitrogen – impacts the structure, productivity and biodiversity of ecosystems via a complex cycle of microbially-mediated reactions. Methionine – the initiating amino acid in protein synthesis – is fundamental to all cells and has been a regulator for the growth of organisms throughout evolution.

Since the beginning of science, improvements in measurements have led to discoveries. We are developing a new generation of isotope analytics  that is based on ESI-Orbitrap mass spectrometry. This technique is opening detailed new views into natural processes. In particular it can reveal the history of a chemical compound, for example the origins of building blocks and the process by which they have been combined.

The overarching aim of my research program is to reveal detailed biological information that is stored within molecules. This aspect of biology is called "intramolecular biology."
ONGOING PROJECTS

​​- Unlocking novel isotopocule signatures of nitrate

- How much of the methionine in humans is industrially synthesized?
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- Technology development for intramolecular biology
IsoX
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The IsoX software (Isotopolog data eXtraction from Orbitrap RAW files) is freely available upon request. Information on how to obtain and use the small tool can be found here. Please email me if you have questions, bug reports or feature requests. 

IsoXL (Isotopologs to eXceL) is a web based interface to process and analyze data from IsoX.
PUBLICATIONS
  1. Kantnerová K, Kuhlbusch N, Juchelka D, Hilkert A, Kopf SH, Neubauer C (in review) ESI-Orbitrap IRMS: A guide to precision isotopocule analysis for life and environmental scientists.
  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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