Pan-Omics Technology Development, Implementation, and Application to GSP Systems Biology Research
EMSL Project ID
48680
Abstract
The BER Genome Science Program aims to understand complex biological and environmental systems across spatial and temporal scales to develop predictive knowledge relevant to DOE mission challenges. Obtaining such systems-level understanding requires multiple broad and high-throughput -omics analytical capabilities. This project aims to facilitate BER research goals by implementing and applying advanced capabilities that are extended to cover important post- translational protein modifications as well as broad measurements of metabolites, lipids, and glycans. Together with more widely available genomics and transcriptomics resources, this project will provide the transformative “pan-omics” measurement capabilities needed to elucidate interacting networks of genes, proteins, and biochemical reactions in biological systems. New measurement platforms and integrated analytical strategies will be implemented in concert with computational advances necessary for handling increased data production rates, improved data processing algorithms, the development of methods to integrate multiple pan- omics data streams, and efforts needed to effectively disseminate results and information to collaborators and the broader scientific community. Developments will continue to be driven by and applied in the context of external collaborative projects aimed at garnering the knowledge needed to lay a foundation for predicting behaviors of and manipulating biological systems critical to DOE missions, including studies of microbial communities, photosynthetic eukaryotes, and eukaryote-prokaryote interactions (e.g., plant interactions with rhizobium symbionts).
Project Details
Start Date
2014-11-10
End Date
2017-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM)
Deng L., V. Garimella, A.M. Hamid, I.K. Webb, I.K. Attah, R.V. Norheim, and S.A. Prost, et al. 2017. "Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM)." Analytical Chemistry 89, no. 12:6432-6439. PNNL-SA-123357. doi:10.1021/acs.analchem.7b00189
Utilizing ion mobility spectrometry and mass spectrometry for the analysis of polycyclic aromatic hydrocarbons, polychlorinated biphenyls, polybrominated diphenyl ethers and their metabolites
Zheng X., K.T. Dupuis, N.A. Aly, Y. Zhou, F.B. Smith, K. Tang, and R.D. Smith, et al. 2018. "Utilizing Ion Mobility Spectrometry and Mass Spectrometry for the Analysis of Polycyclic Aromatic Hydrocarbons, Polychlorinated Biphenyls, Polybrominated Diphenyl Ethers and Their Metabolites." Analytical Chimica Acta 1037. PNNL-SA-130591. doi:10.1016/j.aca.2018.02.054
Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses
Zheng X., R. Wojcik, X. Zhang, Y.M. Ibrahim, K.E. Burnum-Johnson, D.J. Orton, and M.E. Monroe, et al. 2017. "Coupling Front-end Separations, Ion Mobility Spectrometry, and Mass Spectrometry for Enhanced Multidimensional Biological and Environmental Analyses." Annual Review of Analytical Chemistry 10. PNNL-SA-121198. doi:10.1146/annurev-anchem-061516-045212
New frontiers for mass spectrometry based upon structures for lossless ion manipulations
Ibrahim Y.M., A.M. Hamid, L. Deng, V. Garimella, I.K. Webb, E.M. Baker, and R.D. Smith. 2017. "New Frontiers for Mass Spectrometry based upon Structures for Lossless Ion Manipulations." Analyst 142, no. 7:1010-1021. PNNL-SA-123137. doi:10.1039/C7AN00031F
SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids
Zhang X., M.V. Romm, X. Zheng, E.M. Zink, Y. Kim, K.E. Burnum-Johnson, and D.J. Orton, et al. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2. PNNL-SA-117436. doi:10.1016/j.clinms.2016.11.002
The MPLEx Protocol for Multi-omic Analyses of Soil Samples
Nicora C.D., K.E. Burnum-Johnson, E.S. Nakayasu, C.P. Casey, R.A. White, T. Roy Chowdhury, and J.E. Kyle, et al. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343, no. 135. PNNL-SA-129344. doi:10.3791/57343
Characterization of applied fields for ion mobility separations in traveling wave based structures for lossless ion manipulations (SLIM)
Hamid A.M., A. Prabhakaran Nair Syamala Amma, V. Garimella, Y.M. Ibrahim, and R.D. Smith. 2018. "Characterization of applied fields for ion mobility in traveling wave based structures for lossless ion manipulations (SLIM)." International Journal of Mass Spectrometry 430. PNNL-SA-127372. doi:10.1016/j.ijms.2018.03.006
An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies
Bilbao Pena A., B.C. Gibbons, G.W. Slysz, K.L. Crowell, M.E. Monroe, Y.M. Ibrahim, and R.D. Smith, et al. 2018. "An Algorithm to Correct Saturated Mass Spectrometry Ion Abundances for Enhanced Quantitation and Mass Accuracy in Omic Studies." International Journal of Mass Spectrometry 427. PNNL-SA-126312. doi:10.1016/j.ijms.2017.11.003
Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches
Zheng X, RD Smith, and EM Baker. 2018. "Recent Advances in Lipid Separations and Structural Elucidation Using Mass Spectrometry Combined with Ion Mobility Spectrometry, Ion-Molecule Reactions and Fragmentation Approaches." Current Opinion in Chemical Biology 42:111-118. doi:10.1016/j.cbpa.2017.11.009
Comprehensive computational design of ordered peptide macrocycles
Hosseinzadeh P, G Bhardwaj, VK Mulligan, MD Shortridge, TW Craven, F Pardo-Avila, SA Rettie, DE Kim, DA Silva, YM Ibrahim, IK Webb, JR Cort, JN Adkins, G Varani, and D Baker. 2017. "Comprehensive computational design of ordered peptide macrocycles." Science 358(6369):1461-1466. doi:10.1126/science.aap7577
A multi-omic future for microbiome studies
Jansson JK, and ES Baker. 2016. "A multi-omic future for microbiome studies." Nature Microbiology 1(5):Article No. 16049. doi:10.1038/NMICROBIOL.2016.49
Profiling microbial lignocellulose degradation and utilization by emergent omics technologies
Rosnow JJ, LN Anderson, RN Nair, ES Baker, and AT Wright. 2017. "Profiling Microbial Lignocellulose Degradation and Utilization by Emergent Omics Technologies." Critical Reviews in Biotechnology 37(5):626-640. doi:10.1080/07388551.2016.1209158
Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions
Garimella VBS, IK Webb, A Prabhakaran Nair Syamala Amma, IK Attah, YM Ibrahim, and RD Smith. 2017. "DESIGN OF TW-SLIM FOR DUAL POLARITY CONFINEMENT, TRANSPORT AND REACTIONS." Journal of the American Society for Mass Spectrometry 28(7):1442-1449. doi:10.1007/s13361-017-1680-5
Informed-Proteomics: open-source software package for top-down proteomics
Park JK, PD Piehowski, CS Wilkins, M Zhou, JA Mendoza, GM Fujimoto, Y Shen, AK Shukla, RJ Moore, T Liu, VA Petyuk, N Tolic, L Pasa Tolic, RD Smith, SH Payne, and S Kim. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14:909-914. doi:10.1038/nmeth.4388
Distinguishing d- and l-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry
Zheng X, L Deng, EM Baker, YM Ibrahim, VA Petyuk, and RD Smith. 2017. "Distinguishing D- and L-Aspartic and Isoaspartic Acids in Amyloid ? Peptides with Ultrahigh Resolution Ion Mobility Spectrometry." Chemical Communications 53(56):7913-7916. doi:10.1039/C7CC03321D
Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations Using Compression Ratio Ion Mobility Programming
Garimella VBS, AM Hamid, L Deng, YM Ibrahim, IK Webb, EM Baker, SA Prost, RV Norheim, GA Anderson, and RD Smith. 2016. "Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations using Compression Ratio Ion Mobility Programming." Analytical Chemistry 88(23):11877-11885. doi:10.1021/acs.analchem.6b03660
Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry
Burnum-Johnson KE, S Nie, CP Casey, ME Monroe, DJ Orton, YM Ibrahim, MA Gritsenko, TRW Clauss, AK Shukla, RJ Moore, SO Purvine, T Shi, W Qian, T Liu, ES Baker, and RD Smith. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15(12):3694-3705. doi:10.1074/mcp.M116.061143
Ion Elevators and Escalators in Multilevel Structures for Lossless Ion Manipulations
Ibrahim YM, AM Hamid, JT Cox, VBS Garimella, and RD Smith. 2017. "Ion Elevators and Escalators in Multi-level Structures for Lossless Ion Manipulations." Analytical Chemistry 89(3):1972-1977. doi:10.1021/acs.analchem.6b04500
Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations
Wojcik R, IK Webb, VBS Garimella, SA Prost, YM Ibrahim, EM Baker, and RD Smith. 2017. "Lipid and Glycolipid Isomer Analyses Using Ultra-high Resolution Ion Mobility Spectrometry Separations." International Journal of Molecular Sciences 18(1):183. doi:10.3390/ijms18010183
Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations
Deng L, IK Webb, VBS Garimella, AM Hamid, X Zheng, RV Norheim, SA Prost, GA Anderson, JA Sandoval, EM Baker, YM Ibrahim, and RD Smith. 2017. "Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations." Analytical Chemistry 89(8):4628–4634. doi:10.1021/acs.analchem.7b00185
Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry
Zheng X, RS Renslow, MM Makola, IK Webb, L Deng, DG Thomas, N Govind, YM Ibrahim, MM Kabanda, IA Dubery, HM Heyman, RD Smith, NE Madala, and EM Baker. 2017. "Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry." The Journal of Physical Chemistry Letters 8(7):1381-1388. doi:10.1021/acs.jpclett.6b03015
Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies
Kyle JE, CP Casey, KG Stratton, EM Zink, YM Kim, X Zheng, ME Monroe, KK Weitz, KJ Bloodsworth, DJ Orton, YM Ibrahim, RJ Moore, C Lee, C Pedersen, ES Orwoll, RD Smith, KE Burnum-Johnson, and EM Baker. 2017. "Comparing Identified and Statistically Significant Lipids and Metabolites in 15-Year Old Serum and Dried Blood Spot Samples for Longitudinal Studies." Rapid Communications in Mass Spectrometry 31(5):447-456. doi:10.1002/rcm.7808
The fungal cultivar of leaf‐cutter ants produces specific enzymes in response to different plant substrates
Khadempour L, KE Burnum-Johnson, ES Baker, CD Nicora, BJM Webb-Robertson, RA White, III, ME Monroe, EL Huang, RD Smith, and CR Currie. 2016. "The fungal cultivar of leaf?cutter ants produces specific enzymes in response to different plant substrates." Molecular Ecology 25(22):5795-5805. doi:10.1111/mec.13872
Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform
Ibrahim YM, VBS Garimella, SA Prost, R Wojcik, RV Norheim, EM Baker, I Rusyn, and RD Smith. 2016. "Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform." Analytical Chemistry 88(24):12152-12160. doi:10.1021/acs.analchem.6b03027
The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol
Sun J, JD Todd, JC Thrash, Y Qian, MC Qian, B Temperton, J Guo, EMK Fowler, JT Aldrich, CD Nicora, MS Lipton, RD Smith, P De Leenheer, SH Payne, AW Johnston, CL Davie-Martin, KH Halsey, and SJ Giovannoni. 2016. "The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol." Nature Microbiology 1(8):Article No. 16065. doi:10.1038/nmicrobiol.2016.65
Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses
Zheng X, X Zhang, N Schocker, RS Renslow, DJ Orton, J Khamsi, RA Ashmus, IC Almeida, K Tang, CE Costello, RD Smith, K Michael, and EM Baker. 2017. "Enhancing Glycan Isomer Separations with Metal Ions and Positive and Negative Polarity Ion Mobility Spectrometry-Mass Spectrometry Analyses." Analytical and Bioanalytical Chemistry 409:467-476. doi:10.1007/s00216-016-9866-4
MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses
Nakayasu E S,Nicora C D,Sims A C,Burnum-Johnson K E,Kim YM ,Kyle J E,Matzke M M,Shukla A K,Chu R K,Schepmoes A A,Jacobs J M,Baric R ,Webb-Robertson BJ M,Smith R D,Metz T O 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses" mSystems 1(3):e00043-16. 10.1128/mSystems.00043-16
Quantifying Kinase-Specific Phosphorylation Stoichiometry Using Stable Isotope Labeling In a Reverse In-Gel Kinase Assay
Li X ,Cox J T,Tang K ,Bieberich C J 2016. "Quantifying Kinase-specific Phosphorylation Stoichiometry Using Stable Isotope Labeling In a Reverse In-gel Kinase Assay" Analytical Chemistry 88():11468-11475. 10.1021/acs.analchem.6b02599
Dinitrogenase-Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. Strain ATCC 51142
Sadler N C,Bernstein H C,Melnicki M R,Charania M A,Hill E A,Anderson L N,Monroe M E,Smith R D,Beliaev A S,Wright A T 2016. "Dinitrogenase Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. ATCC 51142" Applied Environmental Microbiology 82(24):7227-7235. 10.1128/AEM.02098-16
Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations
Deng L ,Ibrahim Y M,Garimella VBS ,Webb I K,Hamid A M,Norheim R V,Prost S A,Sandoval J A,Baker E M,Smith R D 2016. "Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations" Analytical Chemistry 88(20):10143–10150. 10.1021/acs.analchem.6b02678
Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module
Deng L, YM Ibrahim, AM Hamid, VBS Garimella, IK Webb, X Zheng, SA Prost, JA Sandoval, RV Norheim, GA Anderson, AV Tolmachev, ES Baker, and RD Smith. 2016. "Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13-m Serpentine Path Length Structures for Lossless Ion Manipulations Module." Analytical Chemistry. doi:10. 1021/acs. analchem. 6b01915
Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry
Deng L, YM Ibrahim, ES Baker, NA Aly, AM Hamid, X Zhang, X Zheng, VBS Garimella, IK Webb, SA Prost, JA Sandoval, RV Norheim, GA Anderson, AV Tolmachev, and RD Smith. 2016. "Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry." ChemistrySelect 1(10):2396-2399. doi:10. 1002/slct. 201600460
Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations
Hamid AM, VBS Garimella, YM Ibrahim, L Deng, X Zheng, IK Webb, GA Anderson, SA Prost, RV Norheim, AV Tolmachev, ES Baker, and RD Smith. 2016. "Achieving high resolution ion mobility separations using traveling waves in compact multi-turn Structures for Lossless Ion Manipulations modules." Analytical Chemistry. doi:10. 1021/acs. analchem. 6b01914
A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation
Webb IK, VBS Garimella, RV Norheim, ES Baker, YM Ibrahim, and RD Smith. 2016. "A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation." Journal of the American Society for Mass Spectrometry 2016(27):1285-1288. doi:10.1007/s13361-016-1397-x
Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry
Kyle JE, X Zhang, KK Weitz, ME Monroe, YM Ibrahim, RJ Moore, J Cha, X Sun, ES Lovelace, J Wagoner, S Polyak, TO Metz, SK Dey, RD Smith, KE Burnum-Johnson, and ES Baker. 2016. "Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Analyst Epub ahead of print(141):1649-1659. doi:10.1039/C5AN02062J
Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations
Chen TC, YM Ibrahim, IK Webb, VBS Garimella, X Zhang, AM Hamid, L Deng, WE Karnesky, SA Prost, JA Sandoval, RV Norheim, GA Anderson, AV Tolmachev, ES Baker, and RD Smith. 2016. "Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations." Analytical Chemistry 88(3):1728-1733. doi:10.1021/acs.analchem.5b03910
Role of Cytochrome P450 Hydroxylase in the Decreased Accumulation of Vitamin E in Muscle from Turkeys Compared to that from Chickens
Perez DM, ME Richards, R Parker, ME Berres, AT Wright, M Sifri, NC Sadler, N Tatiyaborworntham, and N Li. 2016. "Role of cytochrome P450 hydroxylase in the decreased accumulation of vitamin E in muscle from turkeys compared to that from chickens." Journal of Agricultural and Food Chemistry 64(3):671-80. doi:10.1021/acs.jafc.5b05433
Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions
Anderson LN, PK Koech, AE Plymale, EV Landorf , A Konopka, F Collart, MS Lipton, MF Romine, and AT Wright. 2015. "Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions ." ACS Chemical Biology . doi:10.1021/acschembio.5b00918 [In Press]
Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch
Garimella VBS, YM Ibrahim, IK Webb, AB Ipsen, TC Chen, AV Tolmachev, ES Baker, GA Anderson, and RD Smith. 2015. "ION MANIPULATIONS IN STRUCTURES FOR LOSSLESS ION MANIPULATIONS (SLIM): COMPUTATIONAL EVALUATION OF A 90o TURN AND A SWITCH." Analyst 140(20):6845-6852. doi:10.1039/c5an00844a
Correcting systematic bias and instrument measurement drift with mzRefinery: Fig. 1.
Gibbons BC, MC Chambers, ME Monroe, DL Tabb, and SH Payne. 2015. "Correcting systematic bias and instrument measurement drift with mzRefinery." Bioinformatics 31(23):3838-3840. doi:10.1093/bioinformatics/btv437
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
Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants
Aylward FO, L Khadempour, D Tremmel, BR McDonald, CD Nicora, S Wu, RJ Moore, DJ Orton, ME Monroe, PD Piehowski, SO Purvine, RD Smith, MS Lipton, KE Burnum-Johnson, and CR Currie. 2015. "Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants." PLoS One 10(8):e0134752. doi:10.1371/journal.pone.0134752
An open-source computational and data resource to analyze digital maps of immunopeptidomes
Caron E, L Espona, DJ Kowalewski, H Schuster, N Ternette, A Alpizar, RB Schittenhelm, SH Ramarathinam, CS Lindestam-Arlehamn, CC Koh, L Gillet, A Rabsteyn, P Navarro, S Kim, H Lam, T Sturm, M Marcilla, A Sette, D Campbell, EW Deutsch, RL Moritz, A Purcell, HG Rammensee, S Stevanovic, and R Aebersold. 2015. "An open-source computational and data resource to analyze digital maps of immunopeptidomes." eLife 4:Article No. e07661. doi:10.7554/eLife.07661
Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling
Liu Y, JK Fredrickson, NC Sadler, P Nandhikonda, RD Smith, and AT Wright. 2015. "Advancing Understanding of Microbial Bioenergy Conversion Processes by Activity-Based Protein Profiling." Biotechnology for Biofuels 8(156):, doi:10.1186/s13068-015-0343-7
Enhancing bottom-up and top-down proteomic measurements with ion mobility separations
Baker ES, KE Burnum-Johnson, YM Ibrahim, DJ Orton, ME Monroe, RT Kelly, RJ Moore, X Zhang, R Theberge, CE Costello, and RD Smith. 2015. "Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations." Proteomics epub ahead of print:, doi:10.1002/pmic.201500048
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data
Ting YS, SH Payne, JD Egertson, S Kim, B MacLean, L Kall, R Aebersold, RD Smith, W Noble, and M MacCoss. 2015. "Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data." Molecular and Cellular Proteomics . doi:10.1074/mcp.0114.047035 [In Press]
Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms
Kim YM, S Nowack, M Olsen, E Becraft, JM Wood, V Thiel, I Klapper, M Kuhl, JK Fredrickson, DA Bryant, DM Ward, and TO Metz. 2015. "Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms." Frontiers in Microbiology 6:Article 209. doi:10.3389/fmicb.2015.00209
Changes in Protein Expression Across Laboratory and Field Experiments in Geobacter bemidjiensis
Merkley ED, KC Wrighton, C Castelle, BJ Anderson, MJ Wilkins, V Shah, T Arbour, JN Brown, SW Singer, RD Smith, and MS Lipton. 2014. "Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis." Journal of Proteome Research epub ahead of print:, doi:10.1021/pr500983v