Publications 2012-2014

[2015-present[2012-2014[2009-2011] [2006-2008] [2000-2005] [pre-2000]

Gaston, K.W.; Limbach, P.A.; “Mass Spectrometry for the Identification and Characterization of Modified Nucleosides and Nucleic Acids” RNA Biology (2014) 11 1568-1585. PMID: 25616408. [Link]

Mummadisettia, M.P.; Frankel, L.K.; Bellamy, H.; Sallans, L.; Goettertb, J.S.; Brylinski, M.; Limbach, P.A.; Bricker, T.M.; “Use of protein crosslinking and radiolytic footprinting to elucidate PsbP and PsbQ interactions within higher plant Photosystem II” Proceedings of the National Academy of Sciences, USA. 111 (2014) 16178-16183. PMID: 25349426. [Link]

Wilson, Z.; McGuire, S.; Limbach, P.A.; Doyle, M.; Marzilli, L.; Warner, I.M.; “Diversifying Science, Technology, Engineering, and Mathematics – An empirical inquiry into successful approaches in chemistry” Journal of Chemical Education 91 (2014) 1860–1866. DOI: 10.1021/ed400702v. [Link]

Li, S.; Limbach, P.A.; “Identification of RNA Sequence Isomers by Isotope Labeling and LC-MS/MS” Journal of Mass Spectrometry 49 (2014) 1191-1198. DOI: 10.1002/jms.3449. PMID: 25395135. [Link]

Puri, P.; Wetzel, C.; Saffert, P.; Gaston, K.W.; Russell, S.P.; van der Vlies, P.; Zhang, G.; Limbach, P.A.; Ignatova, Z.; Poolman, B.; “Systematic identification tRNAome and its dynamics in Lactococcus lactis.” Molecular Microbiology 93 (2014) 944-956. DOI: 10.1111/mmi.12710. PMID: 25040919. [Link]    

Zallot, R.; Brochier-Armanet, C.; Gaston, K.W.; Forouhar, F.; Limbach, P.A.; Hunt, J.; de Crécy-Lagard, V.; “The plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family”, ACS Chemical Biology 9 (2014) 1812-1825. DOI: 10.1021/cb500278k. PMID: 24911101. [Link]    

Dator, R.P.; Gaston, K.W.; Limbach, P.A.; “Multiple Enzymatic Digestions and Ion Mobility Separation Improve Quantification of Bacterial Ribosomal Proteins by Data Independent Acquisition Liquid Chromatography−Mass Spectrometry” Analytical Chemistry 86 (2014) 4264-4270. DOI:10.1021/ac404020j PMID: 24738621. PMCID: PMC4014174. [Link]

Wetzel, C.; Li, S.; Limbach, P.A.; “Metabolic De-isotoping for Improved LC-MS Characterization of Modified RNAs” Journal of the American Society for Mass Spectrometry 25 (2014) 1114-1123. DOI:10.1007/s13361-014-0889-9 PMID: 24760295. [Link]

Köhrer, C.; Mandal, D.; Gaston, K.W.; Grosjean, H.; Limbach, P.A.; RajBhandary, U.L.; “Life without tRNAIle-lysidine synthetase: Translation of the isoleucine codon AUA in Bacillus subtilis lacking the canonical tRNA2IleNucleic Acids Research 42 (2014) 1904-1915 PMID: 24194599. [Link]

Wong, S.Y.; Javid, B.; Addepalli, B.; Piszczek, G.; Strader, M.B.; Limbach, P.A.; Barry III, C.E. “Functional Role of Methylation of G518 of the 16S rRNA 530 loop by GidB in Mycobacterium tuberculosisAntimicrobial Agents and Chemotherapy 57 (2013) 6311-6318. DOI:10.1128/AAC.00905-13. PMID: 24100503. [Link]

Clatterbuck Soper, S.F.; Dator, R.P.; Limbach, P.A.; Woodson, S.A.; “In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent remodeling of late assembly intermediates”, Molecular Cell 52 (2013) 506-516. DOI:10.1016/j.molcel.2013.09.020. PMID: 24207057. [Link]
     *Comment in Pyle, A.M. “Coordinating the Party: Assembly Factors and Ribogenesis” Molecular Cell, 52 (2013) 469-470. [Link]

Wetzel, C.; Limbach, P.A.; “The Global Identification of tRNA Isoacceptors by Targeted Tandem Mass Spectrometry”, Analyst 138 (2013) 6063-6072. DOI:10.1039/c3an01224g. PMID: 23954863. [Link]

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. DOI:10.1016/j.jmb.2013.05.018. PMID: 23727144.  [Link]

Nayak, N.; Putnam, A.; Chen, T.; Schäfermeyer, K.R.; Addepalli, B.; Lowenson, J.; Patra, B.; Jankowsky, E.; Perry, S.E.; Dinkins, R.;  Limbach, P.A.; Ray, A.; Clarke, S.G.; Downie, B.; “The DEAD-box RNA helicase, PRH75, is susceptible to isoAsp formation but can be repaired and activity restored by PROTEIN ISOASPARTYL METHYLTRANSFERASE”, The Plant Cell 25 (2013) 2573-86. DOI:10.1105/tpc.113.113456. PMID: 23903319. [Link]

Frankel, L.K.; Sallans, L.; Bellamy, H.; Goettert, J.S.; Limbach, P.A.; Bricker, T.M.; “Radiolytic Mapping of Solvent Contact Surfaces in Photosystem II of Higher Plants: Experimental Identification of Putative Water Channels within the Photosystem” Journal of Biological Chemistry 288 (2013) 23565-23572. DOI:10.1074/jbc.M113.487033. PMID: 23814046. [Link]

Easter, R.N.; Barry, C.G.; Caruso, J.A.; Limbach, P.A.; “Separation and Identification of Phosphorothioate Oligonucleotides by Hydrophilic Interaction Liquid Chromatography Coupled to Electrospray Ionization Mass Spectrometry”, Analytical Methods 5 (2013) 2657-2659. DOI:10.1039/C3AY26519F.  [Link]

Russell, S.P.; Limbach, P.A.; “Evaluating the Reproducibility of Quantifying Modified Nucleosides from Ribonucleic Acids by LC-UV-MS” Journal of Chromatography, B 923–924 (2013)74-82. DOI:10.1016/j.jchromb.2013.02.010.  PMID: 23500350. [Link]

Frankel, L.K.; Sallans, L.; Limbach, P.A.; Bricker, T.M.; “Oxidized Amino Acid Residues in the Vicinity of QA and PheoD1 of the Photosystem II Reaction Center: Putative Generation Sites of Reducing-Side Reactive Oxygen Species” PLoS One. 8 (2013) e58042. doi:10.1371/journal.pone.0058042. PMID: 23469138. PMCID: PMC3585169.  [Link]

Li, S.; Limbach, P.A.; “Comparative Sequencing of Transfer Ribonucleic Acids by Isotope Labeling and Mass Spectrometry”, Analyst 138 (2013) 1386-1394. DOI:10.1039/C2AN36515D. PMID: 23295341. [Link]

Li, S.; Limbach, P.A.; “Method for Comparative Analysis of Ribonucleic Acids Using Isotope Labeling and Mass Spectrometry” Analytical Chemistry 84 (2012) 8607-8613. DOI:10.1021/ac301638c. PMID: 22985222. [Link]

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. DOI:10.1261/rna.035287.112. PMID: 22912484.  [Link]

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 tRNAArgACG demands a relaxation of the wobble rules in plants”, RNA Biology 9 (2012) 1239-1246. DOI:10.4161/rna.21839 PMID: 22922796. [Link]

Frankel, L.K.; Sallans, L.; Limbach, P.A.; Bricker, T.M.; “Identification of Oxidized Amino Acid Residues in the Vincinity of the Mn4CaO5 Cluster of Photosystem II: Implications for the Identification of Oxygen Channels within the Photosystem”, Biochemistry 51 (2012) 6371-6377. DOI:10.1021/bi300650n. PMID: 22827410 PMCID: PMC3448023. [Link]

Catron, B.L.; Caruso, J.A.; Limbach, P.A.; “Selective Detection of Peptide-Oligonucleotide Heteroconjugates Utilizing Capillary HPLC-ICPMS”, Journal of the American Society for Mass Spectrometry. 23 (2012) 1053-1061. DOI:10.1007/s13361-012-0366-2 PMID: 22451333 PMCID: PMC3348256. [Link]

Butterer, A.; Zorc, M.; Castleberry, C.M.; Limbach, P.A.; “Using Immobilized Enzymes to Reduce RNase Contamination in RNase Mapping of Transfer RNAs by Mass Spectrometry”, Analytical and Bioanalytical Chemistry, 402 (2012) 2701-2711. DOI: 10.1007/s00216-012-5741-0. PMID: 22327965. [Link]

Wetzel, C.; Limbach, P.A.; “Global Identification of Transfer RNAs by Liquid Chromatography-Mass Spectrometry”, Journal of Proteomics, 75 (2012) 3450-3464. DOI:10.1016/j.jprot.2011.09.015 PMID: 21982830. [Link]

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, 7 (2012) 300-305. DOI:10.1021/cb200361w PMID: 22032275 PMCID: PMC3289047. [Link]

© Patrick Limbach, University of Cincinnati 2017
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