Researchers at UCD


H. Alexander Ebhardt

Research Fellow

School Of Medicine
Charles Institute
Dublin 4

Tel: +35317166326


H. Alexander Ebhardt obtained his Ph.D. in Molecular Biology and Biochemistry from Simon Fraser University, B.C., Canada investigating endogenous and exogenous small RNAs in a virally infected system (PNAS 2005). While annotating DNA sequencing data, he noticed that not all small RNA sequences perfectly match to their genome of origin. Further investigation into this peculiar phenomena revealed, that these ¿sequencing errors¿ often coincide with post-transcriptional modifications of the RNA base (NAR 2009) and can impact argonate effector complex association of small RNAs (Silence 2010).

During a RiboClub meeting in Sherbrook, Q.C., Canada a question was posed to the audience: How did the RNA World end? Alex hypothesized: With the arrival of RNase A. This in turn underlined the importance of not only studying RNA, but also proteins. Hence, he expanded his expertise to quantitative mass spectrometry and developed a method to rapidly quantify kinetics of conjugating single amino acids to proteins using MALDI (Anal Chem 2009). Depending on the conjugated amino acid, this post-translational modification can also improve fragmentation of peptides in LC-ESI-MS/MS (RCMS 2014). 

As protein networks are comprised of multiple protein entities, Alex used targeted proteomics (or selected reaction monitoring SRM-MS) to quantify proteins in undepleted human cell lysates (Proteomics 2012). Currently most SRM-MS publications are linked to clinical studies (Proteomics 2015) while the proteomics research community is moving towards SWATH-MS (Sci Data. 2014). Using SWATH-MS, Alex quantified various biological systems and is in the process of publishing the results. His research group at SBI focuses on addressing fundamental questions in biochemistry and unmet clinical needs using targeted proteomics (LC-ESI-MS/MS). 

His latest research findings were submitted to the EAU17 (European Association of Urology annual congress) and the thematic session highlighted in the daily conference news and in URO TODAY.



Peer Reviewed Journals

Ebhardt HA, Degen S, Tadini V, Schilb A, Johns N, Greig CA, Fearon KC, Aebersold R, Jacobi C. (2017) 'Comprehensive proteome analysis of human skeletal muscle in cachexia and sarcopenia: A pilot study'. Journal of Cachexia, Sarcopenia and Muscle, [Epub ahead of print] . [DOI] [Details]
Okada H, Ebhardt HA, Vonesch SC, Aebersold R, Hafen E (2016) 'Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster'. Nature Communications, 7 . [DOI] [Details]
Chaulk, S.G., Ebhardt, H.A., Fahlman, R.P. (2015) 'Correlations of microRNA:microRNA expression patterns reveal insights into microRNA clusters and global microRNA expression patterns'. Molecular BioSystems, 12 (1):110-119. Available Online [DOI] [Details]
Ebhardt, H.A., Root, A., Sander, C., Aebersold, R. (2015) 'Applications of targeted proteomics in systems biology and translational medicine'. Proteomics, 15 (18):3193-3208. Available Online [DOI] [Details]
Ebhardt, H.A., Nan, J., Chaulk, S.G., Fahlman, R.P., Aebersold, R. (2014) 'Enzymatic generation of peptides flanked by basic amino acids to obtain MS/MS spectra with 2ÿ sequence coverage'. Rapid Communications in Mass Spectrometry, 28 (24):2735-2743. Available Online [DOI] [Details]
Hobbs, C.K., Leung, M., Tsang, H.H., Ebhardt, H.A. (2014) 'CIG-P: Circular Interaction Graph for Proteomics'. BMC Bioinformatics, :344. Available Online [DOI] [Details]
Rosenberger, G., Koh, C.C., Guo, T., Röst, H.L., Kouvonen, P., Collins, B.C., Heusel, M., Liu, Y., Caron, E., Vichalkovski, A., Faini, M., Schubert, O.T., Faridi, P., Ebhardt, H.A., Matondo, M., Lam, H., Bader, S.L., Campbell, D.S., Deutsch, E.W., Moritz, R.L., Tate, S., Aebersold, R. (2014) 'A repository of assays to quantify 10,000 human proteins by SWATH-MS'. Scientific Data, 1 . Available Online [DOI] [Details]
Kiel, C., Ebhardt, H.A., Burnier, J., Portugal, C., Sabidó, E., Zimmermann, T., Aebersold, R., Serrano, L. (2014) 'Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins'. Journal of Proteome Research, 13 (1):300-313. Available Online [DOI] [Details]
Ebhardt, H.A. (2014) 'Selected reaction monitoring mass spectrometry: A methodology overview'. Methods in Molecular Biology, 1072 :209-222. Available Online [DOI] [Details]
Fung, A.W.S., Ebhardt, H.A., Krishnakumar, K.S., Moore, J., Xu, Z., Strazewski, P., Fahlman, R.P. (2014) 'Probing the leucyl/phenylalanyl trna protein transferase active site with trna substrate analogues'. Protein and Peptide Letters, 21 (7):603-614. Available Online [DOI] [Details]
Ebhardt, H.A., Ovando, M.O., Unrau, P.J. (2012) 'Isolation and biochemical analysis of plant small RNAs'. Methods in molecular biology (Clifton, N.J.), 894 :223-239. Available Online [Details]
Ebhardt, H.A., Sabidó, E., Hüttenhain, R., Collins, B., Aebersold, R. (2012) 'Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate'. Proteomics, 12 (8):1185-1193. Available Online [DOI] [Details]
Ebhardt, H.A., Ovando, M.O., Unrau, P.J. (2012) 'Isolation and biochemical analysis of plant small RNAs'. Methods in Molecular Biology, 894 :223-239. Available Online [DOI] [Details]
Fung, A.W., Ebhardt, H.A., Abeysundara, H., Moore, J., Xu, Z., Fahlman, R.P. (2011) 'An alternative mechanism for the catalysis of peptide bond formation by L/F transferase: Substrate binding and orientation'. Journal of Molecular Biology, 409 (4):617-629. Available Online [DOI] [Details]
Ebhardt, H.A., Fedynak, A., Fahlman, R.P. (2010) 'Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity'. Silence, 1 (1). Available Online [DOI] [Details]
Ebhardt, H.A., Tsang, H.H., Dai, D.C., Liu, Y., Bostan, B., Fahlman, R.P. (2009) 'Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications'. Nucleic Acids Research, 37 (8):2461-2470. Available Online [DOI] [Details]
Ebhardt, H.A., Unrau, P.J. (2009) 'Characterizing multiple exogenous and endogenous small RNA populations in parallel with subfemtomolar sensitivity using a streptavidin gel-shift assay'. RNA, 15 (4):724-731. Available Online [DOI] [Details]
Ebhardt, H.A., Xu, Z., Fung, A.W., Fahlman, R.P. (2009) 'Quantification of the post-translational addition of amino acids to proteins by MALDI-TOF mass spectrometry'. Analytical Chemistry, 81 (5):1937-1943. Available Online [DOI] [Details]
Morin, R.D., Aksay, G., Dolgosheina, E., Ebhardt, H.A., Magrini, V., Mardis, E.R., Sahinalp, S.C., Unrau, P.J. (2008) 'Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa'. Genome Research, 18 (4):571-584. Available Online [DOI] [Details]
Ebhardt, H.A. (2007) 'RNA interference (RNAi) patents and human health related applications of RNAi'. Recent patents on DNA & gene sequences, 1 (2):128-133. Available Online [Details]
Ebhardt, H.A., Wiese, K.C., Unrau, P.J. (2006) 'Ebbie: Automated analysis and storage of small RNA cloning data using a dynamic web server'. BMC Bioinformatics, 7 . Available Online [DOI] [Details]
Ebhardt, H.A., Thi, E.P., Wang, M.-B., Unrau, P.J. (2005) 'Extensive 3⿲ modification of plant small RNAs is modulated by helper component-proteinase expression'. Proceedings of the National Academy of Sciences of the United States of America, 102 (38):13398-13403. Available Online [DOI] [Details]