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
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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
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
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]
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
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
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
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
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Hamid AM, YM Ibrahim, VBS Garimella, IK Webb, L Deng, TC Chen, GA Anderson, SA Prost, RV Norheim, AV Tolmachev, and RD Smith. 2015. "Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations." Analytical Chemistry 87(22):11301-11308. doi:10.1021/acs.analchem.5b02481
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
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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
Lamarche BL, KL Crowell, J Navdeep, VA Petyuk, AR Shah, AD Polpitiya, JD Sandoval, GR Kiebel, ME Monroe, SJ Callister, TO Metz, GA Anderson, and RD Smith. 2013. "MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis." BMC Bioinformatics 14:,
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
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
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
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
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
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
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Qu Y, Wu S, Zhao R, Zink E, Orton DJ, Moore RJ, Meng D, Clauss TRW, Aldrich JT, Lipton MS, Pa?a-Tolić L: Automated immobilized metal affinity chromatography system for enrichment of Escherichia coli phosphoproteome. Electrophoresis 2013, 34:1619-1626.
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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
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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.
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