Limbach Group Biological Mass Spectrometry

[2021 - present] [2018-2020] [2015-2017] [2012-2014] [2009-2011] [2006-2008] [2000-2005] [pre-2000]

Yu, N.; Lobue, P.A..; Cao, X.; Limbach, P.A.; “RNAModMapper: RNA modification mapping software for analysis of liquid chromatography tandem mass spectrometry data”, Analytical Chemistry (2017) 89 10744-10752. DOI: 10.1021/acs.analchem.7b01780 PMID: 28942636. [Link]

Addepalli, B.; Venus, S.; Thakur, P.; Limbach, P.A.; “Novel Ribonuclease activity of Cusativin from Cucumis sativus for mapping nucleoside modifications in RNA” Analytical Bioanalytical Chemistry (2017) 409 5645–5654. DOI: 10.1007/s00216-017-0500-x. PMID: 28730304 PMCID: PMC5709141. [Link]

Bacusmo JM, Orsini SS, Hu J, DeMott M, Thiaville PC, Elfarash A, Paulines MJ, Rojas-Benítez D, Meineke B, Deutsch C, Iwata-Reuyl D, Limbach PA, Dedon PC, Rice KC, Shuman S, de Crécy-Lagard V.; “The t⁶A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans” RNA Biology (2017) 15 508-517. DOI: 10.1080/15476286.2017.1353861 PMID: 28726545 PMCID: PMC6103680. [Link]

Borland, K.; Limbach, P.A.; “Applications and Advantages of Stable Isotope Phosphate Labeling of RNA in Mass Spectrometry” Topics in Current Chemistry (2017) 375 e33 DOI: 10.1007/s41061-017-0121-z PMID: 28285458. [Link]

Ross, R.; Cao, X.; Limbach, P.A.; “Mapping Post-Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry”, Biomolecules (2017) 7 e21 DOI: 10.3390/biom7010021 PMID: 28241457 PMCID: PMC5372733. [Link]

Rubio, M. A. T.; Gaston, K.W.; McKenney, K.M.; Fleming, I.M.C.; Paris, Z.; Kim, H.-S.; Papavasiliou, F.N.; Limbach, P.A.; Alfonzo, J.D.; “Editing and methylation at a single site by functionally interdependent activities”, Nature (2017) 542 494-497. DOI: 10.1038/nature21396 PMID: 28230119 PMCID: PMC5538571. [Link]

Zallot, R.; Ross, R.; Chen, W-H.; Bruner, S.D.; Limbach, P.A.; de Crecy-Lagard, V.; “Identification of a novel epoxyqueuosine reductase family by comparative genomics”, ACS Chemical Biology (2017) 12 844-851 DOI: 10.1021/acschembio.6b01100 PMID: 28128549 PMCID: PMC5495094. [Link]

Paulines, M.J.; Limbach, P.A.; “Stable Isotope Labeling for Improved Comparative Analysis of RNA Digests by Mass Spectrometry” Journal of the American Society for Mass Spectrometry (2017) 28 551-561. DOI: 10.1007/s13361-017-1593-3 PMID: 28105550. [Link]

Addepalli, B.; Limbach, P.A.; “Pseudouridine in the Anticodon of Escherichia coli tRNA-Tyr(QYA) is Catalyzed by the Dual Specifity Enzyme RluF” The Journal of Biological Chemistry (2016) DOI: 10.1074/jbc.M116.747865 [Link]

Limbach, P.A.; Paulines, M.-J.; “Going Global – the New Era of Mapping Modifications in RNA” WIREs RNA (2017) 8 e1367. DOI: 10.1002/wrna.1367. [Link]

Ross, R.; Cao, X.; Yu, N.; Limbach, P.A.; “Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry” Methods (2016) 107 73–78. DOI: 10.1016/j.ymeth.2016.03.016 [Link]

Delatte, B.; Wang, F.; Ngoc, L.V.; Collignon, E.; Bonvin, E.; Deplus, R.; Calonne, E.; Hassabi, B.; Putmans, P.; Awe, W.; Wetzel, C.; Kreher, J.; Soin, R.; Creppe, C.; Limbach, P.; Gueydan, C.; Kruys, V.; Brehm, A.; Minakhina, S.; Defrance, M.; Steward, R.; Fuks, F.; “Transcriptome-wide distribution and function of RNA hydroxymethylcytosine” Science (2016) 351 282-285. doi:10.1126/science.aac5253. PMID: 26816380 [Link]

Wetzel, C.; Limbach, P.A.; “Mass Spectrometry of Modified RNAs: Recent Developments” Analyst (2016) 141 16–23. DOI: 10.1039/c5an01797a [Link]

Thiaville, P.C.; El Yacoubi, B.; Köhrer, C.; Joseph-Thiaville, J.; Deutsch, C.; Iwata-Reuyl, D.; Bacusmo, J.M.; Armengaud, J.; Bessho, Y.; Wetzel, C.; Cao, X.; Limbach, P.A.; RajBhandary, U.L.; de Crécy-Lagard, V.; “Essentiality in Bacteria of threonylcarbamoyladenosine (t⁶A), a universal modification of tRNA” Molecular Microbiology (2015) 98 1199–1221. DOI: 10.1111/mmi.13209 [Link]

Ross, R.; Sauter Jr., A.D.; Limbach, P.A.; “Induction Based Fluidics (IBF) for Droplet-Based Mass Spectrometric Analysis of Oligonucleotides” Journal of Mass Spectrometry (2015) 50 1175-1179. DOI: 10.1002/jms.3636 [Link]

Cao, X.; Limbach, P.A.; “Enhanced Detection of Post-Transcriptional Modifications Using a Mass-Exclusion List Strategy for RNA Modification Mapping by LC-MS/MS” Analytical Chemistry (2015) 87 8433-40. DOI:10.1021/acs.analchem.5b01826. PMID: 26176336. PMCID: PMC4542202 [Link]

Addepalli, B.; Lesner N.P.; Limbach, P.A.; “Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 from Momordica charantia” RNA (2015) 21 1746-56. DOI: 10.1261/rna.052472.115. PMID: 26221047. [Link]

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. DOI:10.1124/jpet.115.225631. PMID: 26022002. [Link]

Li, M.; Addepalli, B.; Chen, Q.; Wang, W.; Limbach, P.A.; LaSalle, J.; Zeng, S.; Huang, M.; Yu, A-Y.; “Chimeric miR-1291 biosynthesized efficiently in E. coli is effective to reduce target gene expression in human carcinoma cells and improve chemosensitivity” Drug Metabolism and Disposition (2015) 43 1129-1136. DOI:10.1124/dmd.115.064493. PMID: 25934574. [Link] 

Sample, P. J. ; Kořený, L.; Paris, Z.; Gaston, K.W.; Rubio, M.A.T.; Fleming, I.M.C.; Hinger, S.; Horáková, E.; Limbach, P.A.; Lukeš, J.; Alfonzo, J.D.; “A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria” Nucleic Acids Research (2015)  43 4262-4273. DOI:10.1093/nar/gkv286. PMID: 25845597. PMCID: PMC4417183. [Link]

Houser, W.H.; Butterer, A.; Addepalli, B.; Limbach, P.A.; “Enzymatic Generation of 3’-Phosphate from 2’,3’-Cyclic Phosphate Endonuclease Digestion Products of Recombinant RNase U2 for Improved LC/MS Analysis of RNAs” Analytical Biochemistry  (2015) 478 52-58. DOI: 10.1016/j.ab.2015.03.016. PMID: 25797349      [Link]

Sample, P.J.; Gaston, K.W.; Alfonzo, J.D.; Limbach, P.A.; “RoboOligo: Software for Mass Spectrometry Data to Support Manual and De Novo Sequencing of Post-transcriptionally Modified Ribonucleic Acids” Nucleic Acids Research  43 e64. DOI:10.1093/nar/gkv145 PMID: 25820423. PMCID: PMC4446411. [Link]