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

Protocol & Lab Updates...


Total tRNA Shipping Requirements

If you have contacted the lab and are preparing total tRNA for shipment and analysis, please follow the protocol that can be downloaded here.

Jun 12, 2014

CMCT Derivatization Conditions

We have identified a typo in an earlier paper on CMCT derivatization for pseuduridine detection by mass spectrometry (Durairaj, A.; Limbach, P.A. “Improving CMC Derivatization of Pseudouridine in RNA for Mass Spectrometric Detection”, Anal. Chim. Acta 612 (2008) 173-181. PMID: 18358863). This paper stated in the Results & Discussion that an 8000:1 mol ratio was optimum, although one can confirm that was not the mole ratio described in the Experimental section. We apologize for this error.  

Our “best” conditions, which are gauged based on compatibility with mass spectrometry (not primer extension assays), are typically around 100 milligrams of CMCT for every 5 milligrams of tRNA. Under those conditions, we can limit non-specific derivatization yet still adequately derivatize pseudouridine for detection by MS.

Prof. Addepalli in the laboratory has been examining a number of other reaction conditions for RNAs beyond tRNAs, including more recent efforts identifying any off-target effects of CMCT. Although his work remains unpublished, you can contact him for more details by email.

May 21, 2014