High-Throughput Proteomics: Applications and Development (PNNL Scope #40601 and #43488)
EMSL Project ID
34708
Abstract
This project involves the application and development of high-throughput proteomics and quantitative measurement capabilities within biological systems. More so, application measurements will be applied to microbial, microbial communities and plant systems in an effort to extend the understanding of these biological systems. In addition, continuing the development of quantitative and high throughput proteomics capabilities at PNNL will aid in all collaborative projects. The overall goal of this project is to provide and apply enhanced proteomic measurements as it relates to several DOE missions. It is believed that through the development of new and advanced technology the quality of applied gene and protein expression becomes more comprehensive. This is highly desirable for use in collaborative efforts as it relates to this and other projects.
Project Details
Start Date
2009-04-23
End Date
2012-04-29
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85
Burnet MC, A Dohnalkova, AP Neumann, MS Lipton, RD Smith, G Suen, and SJ Callister. 2015. "Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85." PLoS One 10(12):e0143809. doi:10.1371/journal.pone.0143809
The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation
Huang EL, FO Aylward, YM Kim, BJM Webb-Robertson, CD Nicora, Z Hu, TO Metz, MS Lipton, RD Smith, CR Currie, and KE Burnum-Johnson. 2014. "The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation." Environmental Microbiology Reports 6(4):389-95. doi:10.1111/1758-2229.12163
Detection and Identification of Heme c-Modified Peptides by Histidine Affinity Chromatography, High-Performance Liquid Chromatography–Mass Spectrometry, and Database Searching
Merkley ED, BJ Anderson, JH Park, SM Belchik, L Shi, ME Monroe, RD Smith, and MS Lipton. 2012. "Detection and Identification of Heme c-Modified Peptides by Histidine Affinity Chromatography, High-Performance Liquid Chromatography-Mass Spectrometry, and Database Searching." Journal of Proteome Research 11(12):6147-58. doi:10.1021/pr3007914.
Improving N-Glycan Coverage using HPLC-MS with Electrospray Ionization at Subambient Pressure
Marginean I, SR Kronewitter, RJ Moore, GW Slysz, ME Monroe, GA Anderson, K Tang, and RD Smith. 2012. "Improving N-Glycan Coverage using HPLC-MS with Electrospray Ionization at Subambient Pressure." Analytical Chemistry 84(21):9208-9213. doi:10.1021/ac301961u
Protein Identification Using Top-Down Spectra
Liu X, Y Sirotkin, Y Shen, GA Anderson, YHS Tsai, YS Ting, DR Goodlett, RD Smith, V Bafna, and PA Pevzner. 2012. "Protein Identification Using Top-Down." Molecular & Cellular Proteomics. MCP 11(6):M111.008524. doi:Epub 2011 Oct. 25
Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically
Cao L, DA Bryant, AA Schepmoes, K Vogl, RD Smith, MS Lipton, and SJ Callister. 2012. "Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically." Photosynthesis Research 110(3):153-168. doi:10.1007/s11120-011-9711-8
Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142
Vu T, S Stolyar, GE Pinchuk, EA Hill, LA Kucek, RN Brown, MS Lipton, AL Osterman, JK Fredrickson, A Konopka, AS Beliaev, and JL Reed. 2012. "Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142." PLoS Computational Biology 8(4):e1002460. doi:10.1371/journal.pcbi.1002460
Regulatory Response to Carbon Starvation in Caulobacter crescentus
Britos LC, E Abeliuk, T Taverner, MS Lipton, H McAdams, and L Shapiro. 2011. "Regulatory Response to Carbon Starvation in Caulobacter crescentus." PLoS One 6(4):e18179. doi:10.1371/journal.pone.0018179
Archaeosortases and Exosortases Are Widely Distributed Systems Linking Membrane Transit with Posttranslational Modification
Haft DH, SH Payne, and JD Selengut. 2012. "Archaeosortases and Exosortases are Widely Distributed Systems Linking Membrane Transit with Posttranslational Modification." Journal of Bacteriology 194(1):36-48. doi:10.1128/JB.06026-11
Separation of a Set of Peptide Sequence Isomers Using Differential Ion Mobility Spectrometry
Shvartsburg AA, AJ Creese, RD Smith, and HJ Cooper. 2011. "Separation of a Set of Peptide Sequence Isomers Using Differential Ion Mobility Spectrometry ." Analytical Chemistry 83(18):6918-6923. doi:10.1021/ac201640d
A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics
Stanley JR, JN Adkins, GW Slysz, ME Monroe, SO Purvine, YV Karpievitch, GA Anderson, RD Smith, and AR Dabney. 2011. "A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics." Analytical Chemistry 83(16):6135-6140. doi:10.1021/ac2009806
UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling
Huang X, AV Tolmachev, Y Shen, M Liu, L Huang, Z Zhang, GA Anderson, RD Smith, WC Chan, S Hinrichs, K Fu, and SJ Ding. 2011. "UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling." Journal of Proteome Research 10(3):1228-1237. doi:10.1021/pr1010058
Rapid and efficient protein digestion using trypsin-coated magnetic nanoparticles under pressure cycles
Lee B, D Lopez-Ferrer, BC Kim, HB Na, YI Park, KK Weitz, MG Warner, T Hyeon, SW Lee, RD Smith, and J Kim. 2011. "Rapid and Efficient Protein Digestion using Trypsin Coated Magnetic Nanoparticles under Pressure Cycles." Proteomics 11(2):309-318. doi:10.1002/pmic.201000378