Computational Scientist
Computational Scientist


Dr. Aivett Bilbao is a computational scientist with the Systems Modeling and Computational Science team in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. She conducts research on computational tools for mass spectrometry-based omics, working directly with experimental biologists and chemists in interdisciplinary teams. She has acquired extensive experience developing software for mass spectrometry using multiple programming languages and technologies. Projects include proteomics and and small molecule (e.g., metabolites and lipids) molecular characterization entailing both algorithm design and software implementation for data from different instruments (time-of-flight, quadrupole, and Fourier transform-based mass analyzers) and analytical separation techniques (liquid chromatography, ion mobility, solid phase extraction, and gas chromatography). 

She earned her PhD from University of Geneva in Switzerland with special interest in data-independent acquisition mass spectrometry. Her bachelor’s degree is in computer engineering from Universidad de Oriente in Venezuela (cum laude) and her MSc studies were focused on machine learning algorithms and statistical methods at Telecom SudParis in France.

Research Interest

  • Computational methods and data science for mass spectrometry related research


  • Postdoc in Computational Mass Spectrometry, PNNL, 2016 – 2019 

  • PhD in Computational Mass Spectrometry, University of Geneva, 2011 – 2015 

  • MSc in Automatic Data Processing, TELECOM SubParis 2009 – 2011 

  • BSc in Computer Engineering, Universidad de Oriente, 2002 – 2007 



Conant, C. R., Attah, I. K., Garimella, S. V., Nagy, G., Bilbao, A., Smith, R. D., & Ibrahim, Y. M. (2020). Evaluation of Waveform Profiles for Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations. Journal of the American Society for Mass Spectrometry. 


Gabelica, V., A. A. Shvartsburg, C. Afonso, P. Barran, J. L. P. Benesch, C. Bleiholder, M. T. Bowers, A. Bilbao, M. F. Bush, J. L. Campbell, I. D. G. Campuzano, T. Causon, B. H. Clowers, C. S. Creaser, E. De Pauw, J. Far, F. Fernandez-Lima, J. C. Fjeldsted, K. Giles, M. Groessl, C. J. Hogan, Jr., S. Hann, H. I. Kim, R. T. Kurulugama, J. C. May, J. A. McLean, K. Pagel, K. Richardson, M. E. Ridgeway, F. Rosu, F. Sobott, K. Thalassinos, S. J. Valentine, and T. Wyttenbach. 2019. “Recommendations for Reporting Ion Mobility Mass Spectrometry Measurements.” Mass Spectrometry Reviews 38 (3): 291-320.  


Bilbao, A. 2018. “Proteomics Mass Spectrometry Data Analysis Tools.” In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, 84-95.  

Bilbao, A., B. C. Gibbons, G. W. Slysz, K. L. Crowell, M. E. Monroe, Y. M. Ibrahim, R. D. Smith, S. H. Payne, and E. S. Baker. 2018. “An Algorithm to Correct Saturated Mass Spectrometry Ion Abundances for Enhanced Quantitation and Mass Accuracy in Omic Studies.” International Journal of Mass Spectrometry 427: 91-99.  

Bilbao, A., and F. Lisacek. 2018. “Bioinformatics Support for Farm Animal Proteomics.” In Proteomics in Domestic Animals: From Farm to Systems Biology, 361-386.  


Allen White, R., M. I. Borkum, A. Rivas-Ubach, A. Bilbao, J. P. Wendler, S. M. Colby, M. Köberl, and C. Jansson. 2017. “From Data to Knowledge: The Future of Multi-Omics Data Analysis for the Rhizosphere.” Rhizosphere 3: 222-229.  

White, R. A., III, A. Rivas-Ubach, M. I. Borkum, M. Köberl, A. Bilbao, S. M. Colby, D. W. Hoyt, K. Bingol, Y. M. Kim, J. P. Wendler, K. K. Hixson, and C. Jansson. 2017. “The State of Rhizospheric Science in the Era of Multi-Omics: A Practical Guide to Omics Technologies.” Rhizosphere 3: 212-221.  

Zheng, X., N. A. Aly, Y. Zhou, K. T. Dupuis, A. Bilbao, V. L. Paurus, D. J. Orton, R. Wilson, S. H. Payne, R. D. Smith, and E. S. Baker. 2017. “A Structural Examination and Collision Cross Section Database for over 500 Metabolites and Xenobiotics Using Drift Tube Ion Mobility Spectrometry.” Chemical Science 8 (11): 7724-7736.