Limbach Group Biological Mass Spectrometry

A Member of the Rieveschl Laboratories for Mass Spectrometry

in the College of Arts & Sciences' Department of Chemistry

RAMM Software Update (v2) now available

RoboOligo Software now available

Learn more about the National Academies Consensus study on Sequencing the Epitranscriptome

Selected Recent Publications

Robert L. Ross, Ningxi Yu, Ruoxia Zhao, Andrew Wood and Patrick A. Limbach. “Automated Identification of Modified Nucleosides during HRAM-LC-MS/MS using a Metabolomics ID Workflow with Neutral Loss Detection” Journal of the American Society for Mass Spectrometry (2023) doi:10.1021/jasms.3c00298.

Manasses Jora, Daniel Corcoran, Gwenn G. Parungao, Peter A. Lobue, Luiz F. L. Oliveira, George Stan, Balasubrahmanyam Addepalli, and Patrick A. Limbach “Higher-Energy Collisional Dissociation Mass Spectral Networks for the Rapid, Semi-automated Characterization of Known and Unknown Ribonucleoside Modifications” Analytical Chemistry (2022) 94(40):13958-13967. doi: 10.1021/acs.analchem.2c03172. PMID: 36174068.

"Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis” Jora M, Borland K, Abernathy S, Zhao R, Kelley M, Kellner S, Addepalli B, Limbach PA. Angew Chem Int Ed Engl. (2021) 60 3961-3966. DOI: 10.1002/anie.202010793. PMID: 33125801

“Oligonucleotide Analysis by Hydrophilic Interaction Liquid Chromatography-Mass Spectrometry in the Absence of Ion-Pair Reagents” P.A. Lobue, M. Jora, B. Addepalli, P.A. Limbach,  Journal of Chromatography A (2019) DOI: 10.1016/j.chroma.2019.02.016. PMID: 30772056.    

“Transfer RNA Modification Profiles and Codon Decoding Strategies in Methanocaldococcus jannaschii” N. Yu, M. Jora, B. Solivio, P. Thakur, C.G. Acevedo-Rocha, L. Randau, V. de Crécy-Lagard, B. Addepalli, P.A. Limbach,  Journal of Bacteriology (2019) 201 e00690-18. DOI: 10.1128/JB.00690-18 PMID: 30745370.

“RNAModMapper: RNA modification mapping software for analysis of mass spectrometry data”, N Yu, C Wetzel, X Cao, PA Limbach, Analytical Chemistry (2017) doi: 10.1021/acs.analchem.7b01780 PMID: 28942636

June 2 - 6, 2024

Future ASMS conference in Anaheim, CA

Upcoming Events

RNA Modifications - Biology

A significant component of our collaborative research revolves around the characterization of enzymes or enzyme complexes that are involved in the posttranscriptional modification of RNA. Selected publications below highlight the diversity of these collaborative projects.

Selected Publications

     •  van Tran, N.; Muller, L.; Ross, R.L.; Lestini, R.; Létoquart, J.; Ulryck, N.; Limbach, P.A.; de Crécy-Lagard, V.; Cianférani, S.; Graille, M.; “Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes” Nucleic Acids Research (2018) 46 8483-8499. PMID: 30010922

     •  Baldridge, K.C.; Maranhao, A.C.; Jora, M.; Quick, M.M.; Brodbelt, J.S.; Limbach, P.A.; Ellington, A.D.; Contreras, L.M.; “Directed evolution of heterologous tRNAs leads to independence from post-transcriptional modifications” ACS Synthetic Biology (2018) 7 1315-1327. PMID: 29694026

     •  Wang, W-P.; Ho, P-Y.; Chen, Q. Addepalli, B.; Limbach, P.A.; Li, M.; Wu, W.; Jilek, J.L.; Qiu, J.; Zhang, H.; Li, T.; Wun, T.; Lam, K.S.; Yu, A-Y.; “Bioengineering novel chimeric microRNA-34a for prodrug cancer therapy: High-yield expression and purification, and structural and functional characterization” The Journal of Pharmacology and Experimental Therapeutics (2015) 354 131-41. PMID: 26022002     

     •  Rodriguez-Hernandez, A.; Spears, J.; Gaston, K.W.; Limbach, P.A.; Gamper, H.; Hou, Y.-M.; Agris, P.; Perona, J.J.; “Structural and mechanistic basis for enhanced translational efficiency by 2-thiouridine at the tRNA anticodon wobble position” Journal of Molecular Biology 425 (2013) 3888-3906. PMID: 23727144    

     •  Guy, M.P.; Podyma, B.M.; Preston, M.A.; Shaheen, H.H.; Krivos, K.L.; Limbach, P.A.; Hopper, A.K.; Phizicky, E.M.; “Distinct Trm7 complexes that direct anticodon loop modifications are required for efficient tRNAPhe function and healthy growth in yeast”, RNA 18 (2012) 1921-1933.  PMID: 22912484 

     •  Aldinger, C.A.; Leisinger, A-K; Gaston, K.W.; Limbach, P.A.; Igloi, G.L.; “The absence of A-to-I editing in the anticodon of plant cytoplasmic tRNAArgACGdemands a relaxation of the wobble rules in plants”, RNA Biology 9 (2012) 1239-1246. PMID: 22922796    

     •  Phillips, G.; Swairjo, M.A.; Gaston, K.W.; Bailly, M.; Iwata-Reuyl, D.; Limbach, P.A.; de Crecy-Lagard, V.; “Diversity of Archaeosine Synthesis in Crenarchaeota”, ACS Chemical Biology(2012) 300-305. PMID: 22032275.    

     •  Mandal, D., Köhrer, C., Su, D., Russell, S.P., Krivos, K., Castleberry, C.M., Blum, P., Limbach, P.A., Söll, D., RajBhandary, U.L. “Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with Adenosine but not with Guanosine”, Proceedings of the National Academy of Sciences, USA 107 (2010) 2872-2877. PMID: 20133752.