A Member of the Rieveschl Laboratories for Mass Spectrometry
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
Research
Modified RNA Sequencing by Mass Spectrometry
A major interest in our lab is to develop mass spectrometry-based assays for the characterization and quantification of mixtures of small RNAs, such as microRNAs and transfer RNAs (tRNAs). By combining isotopic-labeling strategies with unique "signature" endonuclease digestion products, we are able to both identify and quantify complex mixtures of RNAs without resorting to time-consuming separation methods. To understand the variety of possible "signature" digestion products, we are developing new analytical methods for high-throughput RNA sequencing - where these sequencing methods can identify specific locations and identities of post-transcriptionally modified nucleosides. (Learn more...)
Biological Studies of Modified Nucleosides
Another interest in our lab is to examine enzymes that are responsible for the posttranscriptional modification of RNA. These activities are performed collaborative with numerous colleagues all over the world. In addition to characterize RNA substrates that can be modified, our techniques can be used to discern the different modification patterns found in vivo when genes encoding RNA modifying enzymes are deleted. (Learn more…)
Structural Biology of RNA:Protein Complexes
Cellular processes, such as replication, packaging, repair and transcription of DNA, and maturation, transport, and translation of RNA, require extensive interaction of nucleic acids with various proteins. A fundamental prerequisite for understanding the interactions between proteins and nucleic acids is a detailed knowledge of the structure of nucleic acid-protein complexes. Ribosomes are RNP complexes composed of rRNAs and proteins. To help understanding of how ribosomes are formed and the important RNA-protein interactions that must occur to generate functional complexes, our research program in this area uses a variety of E. coli mutants to capture transient complexes that are involved in the pathway of ribosome formation. (Learn more…)
Medical Applications
With new assays, methods and strategies in place that facilitate the characterization of RNAs and RNPs, our newest efforts have included research within areas of medical importance. Examples include a focus on higher throughput screening methods for identifying modified or mutated microRNAs and tRNAs, especially those smaller RNAs known or suspected to be pathologically significant. (Learn more…)