Mass spectrometry analysis of nucleotides/nucleosides
EMSL Project ID
4099
Abstract
We wish to synthesize a number of specifically-labeled DNA oligomers that will be valuable in characterizing the structure and dynamics of damaged DNAs. In order to do this we will isolate 13C and 15N-labeled RNA and DNA from bacterial cells grown in a medium containing isotopically-labeled carbon and nitrogen substrates. The cells are lysed to yield total nucleic acids which necessitates the separation of deoxyribonucleotides (dNMPs) from ribonucleotides (NMPs), and subsequently the separation of the individual nucleotides and ribonucleotides. We wish to confirm the identity of the individual NMPs and rNMPs using mass spectrometry.
Project Details
Project type
Exploratory Research
Start Date
2004-01-09
End Date
2006-02-02
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Aryal UK, CT Lin, JS Kim, TH Heibeck, J Wang, W Qian, and Y Lin. 2012. "Identification of phosphorylated butyrylcholinesterase in human plasma using immunoaffinity purification and mass spectrometry." Analytica Chimica Acta 723:68-75.
Duan J, VK Kodali, MJ Gaffrey, J Guo, RK Chu, DG Camp, II, RD Smith, BD Thrall, and W Qian. 2015. "Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function During Nanoparticle-Induced Oxidative Stress." ACS Nano Epub ahead of print:, doi:10.1021/acsnano.5b05524
Kim JS, ME Monroe, DG Camp, II, RD Smith, and W Qian. 2013. "In-Source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics ." Journal of Proteome Research 12(2):910-916. doi:10.1021/pr300955f.Epub 2013 January 16.
Peppernick SJ, AG Joly, KM Beck, and WP Hess. 2012. "Near-Field Focused Photoemission from Polystyrene Microspheres Studied with Photoemission Electron Microscopy." Journal of Chemical Physics 137(1):124202-1/9. doi:10.1063/1.4730598
Shi T, and W Qian. 2013. "Antibody-free PRISM-SRM for multiplexed protein quantification: Is this the new competition for immunoassays in bioanalysis?" Bioanalysis 5(3):267-269. doi:10.4155/bio.12.336
Shi T, D Su, T Liu, K Tang, DG Camp, II, W Qian, and RD Smith. 2012. "Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics." Proteomics 12(8):1074-1092. doi:10.1002/pmic.201100436
Shi T, J Zhou, MA Gritsenko, M Hossain, DG Camp, II, RD Smith, and W Qian. 2012. "IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomic biomarker discovery." Methods 56(2):246–253. doi:10.1016/j.ymeth.2011.09.001
Shi T, TL Fillmore, X Sun, R Zhao, AA Schepmoes, M Hossain, S Wu, JS Kim, NJ Jones, RJ Moore, L Pasa-Tolic, J Kagan, KD Rodland, T Liu, K Tang, DG Camp, II, RD Smith, and W Qian. 2012. "An antibody-free, targeted mass spectrometry approach for quantification of proteins at low picogram/milliliter levels in human plasma/serum." Proceedings of the National Academy of Sciences of the United States of America. doi:10.1073/pnas.1204366109 [In Press]
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Shi T, X Sun, Y Gao, TL Fillmore, AA Schepmoes, R Zhao, J He, RJ Moore, J Kagan, KD Rodland, T Liu, AY Liu, RD Smith, K Tang, DG Camp, II, and W Qian. 2013. "Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion." Journal of Proteome Research 12(7):3353-3361. doi:10.1021/pr400178v
Shutthanandan V, Z Zhu, ML Stutzman, F Hannon, C Hernandez-Garcia, MI Nandasiri, SVNT Kuchibhatla, S Thevuthasan, and WP Hess. 2012. "Surface Science Analysis of GaAs Photocathodes Following Sustained Electron Beam Delivery." Physical Review Special Topics - Accelerators and Beams 15(6):063501. doi:10.1103/PhysRevSTAB.15.063501
Sigdel TK, Y Gao, J He, A Wang, CD Nicora, TL Fillmore, T Shi, BJM Webb-Robertson, RD Smith, W Qian, O Salvatierra, DG Camp, II, and M Sarwal. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury ." Kidney International 89(6):1244-1252. doi:10. 1016/j. kint. 2015. 12. 049
Su D, AK Shukla, B Chen, JS Kim, ES Nakayasu, Y Qu, UK Aryal, KK Weitz, TRW Clauss, ME Monroe, DG Camp, II, DJ Bigelow, RD Smith, RN Kulkarni, and W Qian. 2013. "Quantitative Site-specific Reactivity Profiling of S-Nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry." Free Radical Biology & Medicine 57:68-78. doi:10.1016/j.freeradbiomed.2012.12.010
Su D, MJ Gaffrey, J Guo, KE Hatchell, RK Chu, TRW Clauss, JT Aldrich, S Wu, SO Purvine, DG Camp, II, RD Smith, BD Thrall, and W Qian. 2013. "Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-Assisted Thiol-affinity Enrichment and Isobaric Labeling." Free Radical Biology & Medicine. doi:10.1016/j.freeradbiomed.2013.12.004
Wu C, J Duan, T Liu, RD Smith, and W Qian. 2016. "Contributions of Immunoaffinity Chromatography to Deep Proteome Profiling of Human Biofluids." Journal of Chromatography B. doi:10.1016/j.jchromb.2016.01.015