Pan-Omics Technology Development, Implementation, and Application to GSP Systems Biology Research
EMSL Project ID
47418
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
2012-04-30
End Date
2014-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Reproducibility and Transparency by Design
Petyuk V.A., L. Gatto, and S.H. Payne. 2019. "Reproducibility and Transparency by Design." Molecular & Cellular Proteomics. MCP 18, no. 8 suppl 1:S202-S204. PNNL-SA-111442. doi:10.1074/mcp.IP119.001567
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
High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics
Shen Y, N Tolic, PD Piehowski, AK Shukla, S Kim, R Zhao, Y Qu, EW Robinson, RD Smith, and L Pasa-Tolic. 2017. "High-Resolution Ultrahigh-Pressure Long Column Reversed-Phase Liquid Chromatography for Top-Down Proteomics." Journal of Chromatography A 1498:99-110. doi:10.1016/j.chroma.2017.01.008
Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification
Keating DH, Y Zhang, IM Ong, S Mcllwain, EH Morales, JA Grass, M Tremaine, W Bothfeld, A Higbee, A Ulbrich, AJ Balloon, MS Westphall, JT Aldrich, MS Lipton, J Kim, OV Moskvin, YV Bukhman, JJ Coon, PJ Kiley, DM Bates, and R Landick. 2014. "Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification." Frontiers in Microbiology 5:Article No. 402. doi:10.3389/fmicb.2014.00402
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
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
Global Analysis of Salmonella Alternative Sigma Factor E on Protein Translation
Li J, ES Nakayasu, CC Overall, R Johnson, AS Kidwai, JE McDermott, C Ansong, F Heffron, E Cambronne, and JN Adkins. 2015. "Global analysis of Salmonella alternative sigma factor E on protein translation." Journal of Proteome Research 14(4):1716-1726. doi:10.1021/pr5010423
Rectangular Ion Funnel: A New Ion Funnel Interface for Structures for Lossless Ion Manipulations
Chen TC, IK Webb, SA Prost, MB Harrer, RV Norheim, K Tang, YM Ibrahim, and RD Smith. 2015. "Rectangular Ion Funnel: A New Ion Funnel Interface for Structures for Lossless Ion Manipulations." Analytical Chemistry 87(1):716-722. doi:10.1021/ac503564c
Identification of proteins capable of metal reduction from the proteome of the Gram‐positive bacterium D esulfotomaculum reducens MI ‐1 using an NADH ‐based activity assay
Otwell AE, R Sherwood, S Zhang, OD Nelson, Z Li, H Lin, SJ Callister, and RE Richardson. 2015. "Metal Reductases from Gram-Positive Metal Reducer." Environmental Microbiology. doi:10.1111/1462-2920.12673
Activity-based protein profiling of microbes
Sadler NC, and AT Wright. 2015. "Activity-Based Protein Profiling of Microbes." Current Opinion in Chemical Biology 24:139-144. doi:10.1016/j.cbpa.2014.10.022
Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer
Chen Y, FE Leach, III, NK Kaiser, X Dang, YM Ibrahim, RV Norheim, GA Anderson, RD Smith, and AG Marshall. 2015. "Improved Ion Optics for Introduction of Ions into a 9.4 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer." Journal of Mass Spectrometry 50(1):280-284. doi:10.1002/jms.3523
Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture
Boaro AA, YM Kim, A Konopka, SJ Callister, and BK Ahring. 2014. "Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture." FEMS Microbiology Ecology 90(3):802-15. doi:10.1111/1574-6941.12435
On the Ionization and Ion Transmission Efficiencies of Different ESI-MS Interfaces
Cox JT, I Marginean, RD Smith, and K Tang. 2014. "On the Ionization and Ion Transmission Efficiencies of Different ESI-MS Interfaces." Journal of the American Society for Mass Spectrometry . doi:10.1007/s13361-014-0998-5 [In Press]
Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides
Pena-Castillo L, R Mercer, A Gurinovich, SJ Callister, AT Wright, A Westbye, JT Beatty, and AS Lang. 2014. "Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides ." BMC Genomics 15(730):, doi:10.1186/1471-2164-15-730
Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid
Hyung SW, RJ Moore, PD Piehowski, DJ Orton, AA Schepmoes, TRW Clauss, RK Chu, TL Fillmore, HM Brewer, T Liu, R Zhao, and RD Smith. 2014. "Micro-Scale Depletion of High Abundance Proteins in Human Bio-fluids using IgY14 Immunoaffinity Resin: Analysis of Human Plasma and Cerebrospinal Fluid ." Journal of Proteome Research Epub ahead of print:, doi:10.1007/s00216-014-8058-3
Polysialylated N-Glycans Identified in Human Serum Through Combined Developments in Sample Preparation, Separations, and Electrospray Ionization-Mass Spectrometry
Kronewitter SR, I Marginean, JT Cox, R Zhao, CD Hagler, AK Shukla, TS Carlson, JN Adkins, DG Camp, II, RJ Moore, KD Rodland, and RD Smith. 2014. "Polysialylated N-Glycans Identified in Human Serum Through Combined Developments in Sample Preparation, Separations and Electrospray ionization-mass spectrometry." Analytical Chemistry 86(17):8700-10. doi:10.1021/ac501839b
Proteogenomic characterization of human colon and rectal cancer
Zhang B, J Wang, wang, J Zhu, Q Liu, Z Shi, MC Chambers, LJ Zimmerman, KF Shaddox, S Kim, S Davies, C Kinsinger, R Rivers, H Rodriguez, R Townsend, M Ellis, SA Carr, DL Tabb, RJ Coffey, R Slebos, and D Liebler. 2014. "Proteogenomic characterization of human colon and rectal cancer." Nature ePub ahead of print:, doi:10.1038/nature13438
GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization
Kronewitter SR, GW Slysz, I Marginean, CD Hagler, BL Lamarche, R Zhao, MY Harris, ME Monroe, CA Polyukh, KL Crowell, TL Fillmore, TS Carlson, DG Camp, II, RJ Moore, SH Payne, GA Anderson, and RD Smith. 2014. "GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization." Analytical Chemistry 86(13):6268-6276. doi:10.1021/ac501492f
Proteomic Profiles of Five Strains of Oxygenic Photosynthetic Cyanobacteria of the Genus Cyanothece
Aryal UK, SJ Callister, BH McMahon, LA McCue, JN Brown, J Stockel, ML Liberton, S Mishra, X Zhang, CD Nicora, TE Angel, DW Koppenaal, RD Smith, HB Pakrasi, and L Sherman. 2014. "Proteomic screens of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece." Journal of Proteome Research EPub as 'Just Accepted':, doi:10.1021/pr5000889
Spectral probabilities of top-down tandem mass spectra
Liu X, MW Segar, SC Li, and S Kim. 2014. "Spectral probabilities of top-down tandem mass spectra." BMC Genomics 15(Suppl 1):S9 . doi:10.1186/1471-2164-15-S1-S9
Expanding Proteome Coverage with Orthogonal-specificity α-Lytic Proteases
Meyer JG, S Kim, DA Maltby, N Bandeira, and EA Komives. 2014. "Expanding proteome coverage with orthogonal-specificity a-Lytic proteases ." Molecular & Cellular Proteomics. MCP 13(3):823-35. doi:10.1074/mcp.M113.034710
Differential Ion Mobility Separations in up to 100 % Helium Using Microchips
Shvartsburg AA, YM Ibrahim, and RD Smith. 2014. "Differential Ion Mobility Separations in up to 100% Helium Using Microchips." Journal of the American Society for Mass Spectrometry 2014(25):480-489. doi:10.1007/s13361-013-0797-4
Signatures for Mass Spectrometry Data Quality
Amidan BG, DJ Orton, BL Lamarche, ME Monroe, RJ Moore, RD Smith, LH Sego, SH Payne, and MF Tardiff. 2014. "Signatures for Mass Spectrometry Data Quality." Journal of Proteome Research. doi:10.1021/pr401143e
Implementation of Dipolar Resonant Excitation for Collision Induced Dissociation with Ion Mobility/Time-of-Flight MS
Webb IK, TC Chen, WF Danielson, III, YM Ibrahim, K Tang, GA Anderson, and RD Smith. 2014. "Implementation of Dipolar Resonant Excitation Collision Induced Dissociation with Ion Mobility/Time-of-Flight MS." Journal of the American Society for Mass Spectrometry 25(4):563-571. doi:10.1007/s13361-013-0815-6
Automated Data Extraction from In Situ Protein-Stable Isotope Probing Studies
Slysz GW, LA Steinke, DM Ward, CG Klatt, TRW Clauss, SO Purvine, SH Payne, GA Anderson, RD Smith, and MS Lipton. 2014. "Automated data extraction from in situ protein stable isotope probing studies." Journal of Proteome Research. doi:10.1021/pr400633j
Fast and Accurate Database Searches with MS-GF+Percolator
Granholm V, S Kim, JC Navarro, E Sjolund, RD Smith, and L Kall. 2013. "Fast and accurate database searches with MS-GF+Percolator." Journal of Proteome Research. doi:10.1021/pr400937n
LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets
Crowell KL, GW Slysz, ES Baker, BL Lamarche, ME Monroe, YM Ibrahim, SH Payne, GA Anderson, and RD Smith. 2013. "LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets." Bioinformatics 29(21):2804-2805 . doi:10.1093/bioinformatics/btt465
Pushing the Frontier of High-Definition Ion Mobility Spectrometry Using FAIMS
Shvartsburg AA, GA Anderson, and RD Smith. 2013. "Pushing the Frontier of High-Definition Ion Mobility Spectrometry Using FAIMS." Mass Spectrometry Society of Japan. Journal 2:Article No. S0011. doi:10.5702/massspectrometry.S0011
Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans
Wu S, RN Brown, SH Payne, D Meng, R Zhao, N Tolic, L Cao, AK Shukla, ME Monroe, RJ Moore, MS Lipton, and L Pasa-Tolic. 2013. "Top-down characterization of the post-translationally modified intact periplasmic proteome of the bacterium Novosphingobium aromaticivorans ." International Journal of Proteomics 2013:279590. doi:10.1155/2013/279590.
Increasing confidence of LC–MS identifications by utilizing ion mobility spectrometry
Crowell KL, ES Baker, SH Payne, YM Ibrahim, ME Monroe, GW Slysz, BL Lamarche, VA Petyuk, PD Piehowski, WF Danielson, III, GA Anderson, and RD Smith. 2013. "Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry." International Journal of Mass Spectrometry. doi:10.1016/j.ijms.2013.06.028