Richard Dale Smith - Publications

Affiliations: 
Pacific Northwest National Laboratory, USA 

229 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Dou M, Clair G, Tsai CF, Xu K, Chrisler WB, Sontag RL, Zhao R, Moore RJ, Liu T, Paša-Tolić L, Smith RD, Shi T, Adkins JN, Qian WJ, Kelly RT, et al. High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform. Analytical Chemistry. PMID 31509397 DOI: 10.1021/acs.analchem.9b03349  0.32
2019 Wojcik R, Nagy G, Attah IK, Webb I, Garimella SVB, Weitz KK, Hollerbach A, Monroe ME, Ligare MR, Nielson FF, Norheim RV, Renslow RS, Metz TO, Ibrahim YM, Smith RD. SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes. Analytical Chemistry. PMID 31450886 DOI: 10.1021/acs.analchem.9b02808  0.72
2019 Nagarajan A, Zhou M, Nguyen AY, Liberton M, Kedia K, Shi T, Piehowski P, Shukla A, Fillmore TL, Nicora C, Smith RD, Koppenaal DW, Jacobs JM, Pakrasi HB. Proteomic Insights into Phycobilisome Degradation, A Selective and Tightly Controlled Process in The Fast-Growing Cyanobacterium UTEX 2973. Biomolecules. 9. PMID 31426316 DOI: 10.3390/biom9080374  0.32
2019 Dirice E, Kahraman S, De Jesus DF, El Ouaamari A, Basile G, Baker RL, Yigit B, Piehowski PD, Kim MJ, Dwyer AJ, Ng RWS, Schuster C, Vethe H, Martinov T, Ishikawa Y, ... ... Smith RD, et al. Increased β-cell proliferation before immune cell invasion prevents progression of type 1 diabetes. Nature Metabolism. 1: 509-518. PMID 31423480 DOI: 10.1038/s42255-019-0061-8  0.32
2019 Tsai CF, Smith J, Krajewski K, Zhao R, Moghieb AM, Nicora CD, Xiong X, Moore RJ, Liu T, Smith RD, Jacobs JM, Rajagopal S, Shi T. TMT labeling facilitates RPLC-MS analysis of hydrophilic phosphopeptides. Analytical Chemistry. PMID 31418558 DOI: 10.1021/acs.analchem.9b01814  0.36
2019 Zhang Y, Zhong Y, Connor AL, Miller DP, Cao R, Shen J, Song B, Baker ES, Tang Q, Pulavarti SVSRK, Liu R, Wang Q, Lu ZL, Szyperski T, Zeng H, ... ... Smith RD, et al. Folding and Assembly of Short α, β, γ-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures. Journal of the American Chemical Society. PMID 31381306 DOI: 10.1021/jacs.9b06094  0.44
2019 Dou M, Tsai CF, Piehowski PD, Wang Y, Fillmore TL, Zhao R, Moore RJ, Zhang P, Qian WJ, Smith RD, Liu T, Kelly RT, Shi T, Zhu Y. Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples. Analytical Chemistry. PMID 31241912 DOI: 10.1021/acs.analchem.9b01248  0.48
2019 Zheng X, Smith FB, Aly NA, Cai J, Smith RD, Patterson AD, Baker ES. Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry. Analytical and Bioanalytical Chemistry. PMID 31098744 DOI: 10.1007/s00216-019-01869-0  0.44
2019 Moghieb A, Tesfay L, Nie S, Gritsenko M, Fillmore TL, Jacobs JM, Smith RD, Torti FM, Torti SV, Shi T, Ansong C. A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification. Scientific Reports. 9: 7264. PMID 31086210 DOI: 10.1038/s41598-019-43756-9  0.32
2019 Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, ... ... Smith RD, et al. Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities. Cell. PMID 31031003 DOI: 10.1016/j.cell.2019.03.030  0.48
2019 Yi L, Tsai CF, Dirice E, Swensen AC, Chen J, Shi T, Gritsenko MA, Chu RK, Piehowski PD, Smith RD, Rodland KD, Atkinson MA, Mathews CE, Kulkarni RN, Liu T, et al. A Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells. Analytical Chemistry. PMID 30843680 DOI: 10.1021/acs.analchem.9b00024  0.48
2019 Attah IK, Garimella SVB, Webb IK, Nagy G, Norheim RV, Schimelfenig CE, Ibrahim YM, Smith RD. Dual Polarity Ion Confinement and Mobility Separations. Journal of the American Society For Mass Spectrometry. PMID 30834510 DOI: 10.1007/s13361-019-02138-1  0.4
2019 Wakasaki R, Matsushita K, Golgotiu K, Anderson S, Eiwaz MB, Orton DJ, Han SJ, Lee HT, Smith RD, Rodland KD, Piehowski PD, Hutchens MP. Glomerular filtrate proteins in acute cardiorenal syndrome. Jci Insight. 4. PMID 30829647 DOI: 10.1172/jci.insight.122130  0.48
2019 Nagy G, Kedia K, Attah IK, Garimella SVB, Ibrahim YM, Petyuk VA, Smith RD. Separation of β-Amyloid Tryptic Peptide Species with Isomerized and Racemized L-Aspartic Residues with Ion Mobility in Structures for Lossless Ion Manipulations. Analytical Chemistry. PMID 30816701 DOI: 10.1021/acs.analchem.8b04696  0.4
2018 Hamid AM, Prabhakaran A, Garimella SVB, Ibrahim YM, Smith RD. Characterization of applied fields for ion mobility separations in traveling wave based structures for lossless ion manipulations (SLIM). International Journal of Mass Spectrometry. 430: 8-13. PMID 31467482 DOI: 10.1016/j.ijms.2018.03.006  0.4
2018 Zhang P, Gaffrey MJ, Zhu Y, Chrisler WB, Fillmore TL, Yi L, Nicora CD, Zhang T, Wu H, Jacobs JM, Tang K, Kagan J, Srivastava S, Rodland KD, Qian WJ, ... Smith RD, et al. Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells. Analytical Chemistry. PMID 30557009 DOI: 10.1021/acs.analchem.8b04258  0.4
2018 Nagy G, Veličković D, Chu RK, Carrell AA, Weston DJ, Ibrahim YM, Anderton CR, Smith RD. Towards resolving the spatial metabolome with unambiguous molecular annotations in complex biological systems by coupling mass spectrometry imaging with structures for lossless ion manipulations. Chemical Communications (Cambridge, England). PMID 30534702 DOI: 10.1039/c8cc07482h  0.4
2018 Dou M, Chouinard CD, Zhu Y, Nagy G, Liyu AV, Ibrahim YM, Smith RD, Kelly RT. Nanowell-mediated multidimensional separations combining nanoLC with SLIM IM-MS for rapid, high-peak-capacity proteomic analyses. Analytical and Bioanalytical Chemistry. PMID 30397757 DOI: 10.1007/s00216-018-1452-5  0.4
2018 Matsushita K, Golgotiu K, Orton DJ, Smith RD, Rodland KD, Piehowski PD, Hutchens MP. Micropuncture of Bowman's Space in Mice Facilitated by 2 Photon Microscopy. Journal of Visualized Experiments : Jove. PMID 30371667 DOI: 10.3791/58206  0.48
2018 Zheng X, Dupuis KT, Aly NA, Zhou Y, Smith FB, Tang K, Smith RD, Baker ES. Utilizing ion mobility spectrometry and mass spectrometry for the analysis of polycyclic aromatic hydrocarbons, polychlorinated biphenyls, polybrominated diphenyl ethers and their metabolites. Analytica Chimica Acta. 1037: 265-273. PMID 30292301 DOI: 10.1016/j.aca.2018.02.054  0.44
2018 Shi T, Gaffrey MJ, Fillmore TL, Nicora CD, Yi L, Zhang P, Shukla AK, Wiley HS, Rodland KD, Liu T, Smith RD, Qian WJ. Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells. Communications Biology. 1: 103. PMID 30271983 DOI: 10.1038/s42003-018-0107-6  0.32
2018 Nagy G, Attah IK, Garimella SVB, Tang K, Ibrahim YM, Baker ES, Smith RD. Unraveling the isomeric heterogeneity of glycans: ion mobility separations in structures for lossless ion manipulations. Chemical Communications (Cambridge, England). PMID 30264832 DOI: 10.1039/c8cc06966b  0.44
2018 Kedia K, Wendler JP, Baker ES, Burnum-Johnson KE, Jarsberg LG, Stratton KG, Wright AT, Piehowski PD, Gritsenko MA, Lewinsohn DM, Sigal GB, Weiner MH, Smith RD, Jacobs JM, Nahid P. Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis. Tuberculosis (Edinburgh, Scotland). 112: 52-61. PMID 30205969 DOI: 10.1016/j.tube.2018.07.005  0.48
2018 Nagy G, Chouinard CD, Attah IK, Webb IK, Garimella SVB, Ibrahim YM, Baker ES, Smith RD. Distinguishing enantiomeric amino acids with chiral cyclodextrin adducts and structures for lossless ion manipulations. Electrophoresis. PMID 30168603 DOI: 10.1002/elps.201800294  0.44
2018 Chouinard CD, Nagy G, Webb IK, Shi T, Baker ES, Prost SA, Liu T, Ibrahim YM, Smith RD. Improved Sensitivity and Separations for Phosphopeptides using Online LC Coupled with Structures for Lossless Ion Manipulations (SLIM) IM-MS. Analytical Chemistry. PMID 30118596 DOI: 10.1021/acs.analchem.8b02397  0.44
2018 Chouinard CD, Nagy G, Webb IK, Garimella SVB, Baker ES, Ibrahim YM, Smith RD. Rapid Ion Mobility Separations of Bile Acid Isomers using Cyclodextrin Adducts and Structures for Lossless Ion Manipulations. Analytical Chemistry. PMID 30102518 DOI: 10.1021/acs.analchem.8b02990  0.44
2018 MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES. Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. Journal of the American Society For Mass Spectrometry. PMID 30047074 DOI: 10.1007/s13361-018-2028-5  0.44
2018 Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, Petyuk VA, Thomas SN, Mani DR, Mundt F, Moore RJ, ... ... Smith RD, et al. Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry. Nature Protocols. PMID 29988108 DOI: 10.1038/s41596-018-0006-9  0.48
2018 Zhu Y, Dou M, Piehowski PD, Liang Y, Wang F, Chu RK, Chrisler W, Smith JN, Schwarz KC, Shen Y, Shukla AK, Moore RJ, Smith RD, Qian WJ, Kelly RT. Spatially resolved proteome mapping of laser capture microdissected tissue with automated sample transfer to nanodroplets. Molecular & Cellular Proteomics : McP. PMID 29941660 DOI: 10.1074/mcp.TIR118.000686  0.48
2018 Nicora CD, Burnum-Johnson KE, Nakayasu ES, Casey CP, White RA, Roy Chowdhury T, Kyle JE, Kim YM, Smith RD, Metz TO, Jansson JK, Baker ES. The MPLEx Protocol for Multi-omic Analyses of Soil Samples. Journal of Visualized Experiments : Jove. PMID 29912205 DOI: 10.3791/57343  0.72
2018 Yu L, Petyuk VA, Gaiteri C, Mostafavi S, Young-Pearse T, Shah RC, Buchman AS, Schneider JA, Piehowski PD, Sontag RL, Fillmore TL, Shi T, Smith RD, De Jager PL, Bennett DA. Targeted brain proteomics uncover multiple pathways to Alzheimer's dementia. Annals of Neurology. PMID 29908079 DOI: 10.1002/ana.25266  0.32
2018 Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, ... Smith RD, et al. Author Correction: Informed-Proteomics: open-source software package for top-down proteomics. Nature Methods. PMID 29899368 DOI: 10.1038/s41592-018-0040-0  0.48
2018 Bilbao A, Gibbons BC, Slysz GW, Crowell KL, Monroe ME, Ibrahim YM, Smith RD, Payne SH, Baker ES. An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies. International Journal of Mass Spectrometry. 427: 91-99. PMID 29706793 DOI: 10.1016/j.ijms.2017.11.003  0.44
2018 Stanfill BA, Nakayasu ES, Bramer LM, Thompson AM, Ansong CK, Clauss T, Gritsenko MA, Monroe ME, Moore RJ, Orton DJ, Piehowski PD, Schepmoes AA, Smith RD, Webb-Robertson BJ, Metz TO, et al. QC-ART: A tool for real-time quality control assessment of mass spectrometry-based proteomics data. Molecular & Cellular Proteomics : McP. PMID 29666158 DOI: 10.1074/mcp.RA118.000648  0.72
2018 Yi L, Shi T, Gritsenko MA, Chan CX, Fillmore TL, Hess BM, Swensen AC, Liu T, Smith RD, Wiley HS, Qian WJ. Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway. Analytical Chemistry. PMID 29584399 DOI: 10.1021/acs.analchem.8b00071  0.32
2018 Zhu Y, Zhao R, Piehowski PD, Moore RJ, Lim S, Orphan VJ, Paša-Tolić L, Qian WJ, Smith RD, Kelly RT. Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples. International Journal of Mass Spectrometry. 427: 4-10. PMID 29576737 DOI: 10.1016/j.ijms.2017.08.016  0.48
2018 Kyle JE, Aly N, Zheng X, Burnum-Johnson KE, Smith RD, Baker ES. Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry. Bioanalysis. PMID 29494212 DOI: 10.4155/bio-2017-0245  0.44
2018 Zhu Y, Piehowski PD, Zhao R, Chen J, Shen Y, Moore RJ, Shukla AK, Petyuk VA, Campbell-Thompson M, Mathews CE, Smith RD, Qian WJ, Kelly RT. Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells. Nature Communications. 9: 882. PMID 29491378 DOI: 10.1038/s41467-018-03367-w  0.48
2018 Orwoll ES, Wiedrick J, Jacobs J, Baker ES, Piehowski P, Petyuk V, Gao Y, Shi T, Smith RD, Bauer DC, Cummings SR, Nielson CM, Lapidus J. High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men. Aging Cell. PMID 29399943 DOI: 10.1111/acel.12717  0.44
2018 Menachery VD, Schäfer A, Burnum-Johnson KE, Mitchell HD, Eisfeld AJ, Walters KB, Nicora CD, Purvine SO, Casey CP, Monroe ME, Weitz KK, Stratton KG, Webb-Robertson BM, Gralinski LE, Metz TO, ... Smith RD, et al. MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape. Proceedings of the National Academy of Sciences of the United States of America. PMID 29339515 DOI: 10.1073/pnas.1706928115  0.72
2017 Zheng X, Aly NA, Zhou Y, Dupuis KT, Bilbao A, Paurus VL, Orton DJ, Wilson R, Payne SH, Smith RD, Baker ES. A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry. Chemical Science. 8: 7724-7736. PMID 29568436 DOI: 10.1039/c7sc03464d  0.44
2017 Shi T, Quek SI, Gao Y, Nicora CD, Nie S, Fillmore TL, Liu T, Rodland KD, Smith RD, Leach RJ, Thompson IM, Vitello EA, Ellis WJ, Liu AY, Qian WJ. Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins. Oncotarget. 8: 101887-101898. PMID 29254211 DOI: 10.18632/oncotarget.21710  0.32
2017 Prabhakaran A, Hamid AM, Garimella SVB, Valenzuela BR, Ewing RG, Ibrahim YM, Smith RD. A Hybrid Constant and Oscillatory Field Ion Mobility Analyzer Using Structures for Lossless Ion Manipulations. Journal of the American Society For Mass Spectrometry. PMID 29235041 DOI: 10.1007/s13361-017-1841-6  0.4
2017 Zheng X, Smith RD, Baker ES. 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. PMID 29223060 DOI: 10.1016/j.cbpa.2017.11.009  0.44
2017 Poad BLJ, Zheng X, Mitchell TW, Smith RD, Baker ES, Blanksby SJ. Online ozonolysis combined with ion mobility-mass spectrometry provides a new platform for lipid isomer analyses. Analytical Chemistry. PMID 29220163 DOI: 10.1021/acs.analchem.7b04091  0.44
2017 Orton DJ, Tfaily MM, Moore RJ, LaMarche BL, Zheng X, Fillmore TL, Chu RK, Weitz KK, Monroe ME, Kelly RT, Smith RD, Baker ES. A Customizable Flow Injection System for Automated, High Throughput and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements. Analytical Chemistry. PMID 29161511 DOI: 10.1021/acs.analchem.7b02986  0.48
2017 Eisfeld AJ, Halfmann PJ, Wendler JP, Kyle JE, Burnum-Johnson KE, Peralta Z, Maemura T, Walters KB, Watanabe T, Fukuyama S, Yamashita M, Jacobs JM, Kim YM, Casey CP, Stratton KG, ... ... Smith RD, et al. Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis. Cell Host & Microbe. PMID 29154144 DOI: 10.1016/j.chom.2017.10.011  0.72
2017 Gao Y, Wang H, Nicora CD, Shi T, Smith RD, Sigdel TK, Sarwal MM, Camp DG, Qian WJ. LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers. Methods in Molecular Biology (Clifton, N.J.). PMID 29116567 DOI: 10.1007/7651_2017_93  0.32
2017 Garabedian A, Benigni P, Ramirez CE, Baker ES, Liu T, Smith RD, Fernandez-Lima F. Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS. Journal of the American Society For Mass Spectrometry. PMID 28889248 DOI: 10.1007/s13361-017-1787-8  0.44
2017 Wang H, Barbieri CE, He J, Gao Y, Shi T, Wu C, Schepmoes AA, Fillmore TL, Chae SS, Huang D, Mosquera JM, Qian WJ, Smith RD, Srivastava S, Kagan J, et al. Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics. Journal of Translational Medicine. 15: 175. PMID 28810879 DOI: 10.1186/s12967-017-1276-7  0.32
2017 Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, ... Smith RD, et al. Informed-Proteomics: open-source software package for top-down proteomics. Nature Methods. PMID 28783154 DOI: 10.1038/nmeth.4388  0.48
2017 Yi L, Piehowski PD, Shi T, Smith RD, Qian WJ. Advances in microscale separations towards nanoproteomics applications. Journal of Chromatography. A. PMID 28765000 DOI: 10.1016/j.chroma.2017.07.055  0.32
2017 Stow SM, Causon T, Zheng X, Kurulugama RT, Mairinger T, May JC, Rennie EE, Baker ES, Smith RD, McLean JA, Hann S, Fjeldsted JC. An Interlaboratory Evaluation of Drift Tube Ion Mobility - Mass Spectrometry Collision Cross Section Measurements. Analytical Chemistry. PMID 28763190 DOI: 10.1021/acs.analchem.7b01729  0.44
2017 Nie S, Shi T, Fillmore TL, Schepmoes AA, Brewer H, Gao Y, Song E, Wang H, Rodland KD, Qian WJ, Smith RD, Liu T. Deep-Dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Non-depleted Human Blood Plasma/Serum and Tissues. Analytical Chemistry. PMID 28724286 DOI: 10.1021/acs.analchem.7b01878  0.32
2017 Song E, Gao Y, Wu C, Shi T, Nie S, Fillmore TL, Schepmoes AA, Gritsenko MA, Qian WJ, Smith RD, Rodland KD, Liu T. Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer. Scientific Data. 4: 170091. PMID 28722704 DOI: 10.1038/sdata.2017.91  0.48
2017 Zheng X, Deng L, Baker ES, Ibrahim YM, Petyuk VA, Smith RD. Distinguishing d- and l-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry. Chemical Communications (Cambridge, England). PMID 28654112 DOI: 10.1039/c7cc03321d  0.44
2017 Kerkhoven EJ, Kim YM, Wei S, Nicora CD, Fillmore TL, Purvine SO, Webb-Robertson BJ, Smith RD, Baker SE, Metz TO, Nielsen J. Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica. Mbio. 8. PMID 28634240 DOI: 10.1128/mBio.00857-17  0.72
2017 Garimella SVB, Webb IK, Prabhakaran A, Attah IK, Ibrahim YM, Smith RD. Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions. Journal of the American Society For Mass Spectrometry. PMID 28560562 DOI: 10.1007/s13361-017-1680-5  0.4
2017 Ma J, Casey CP, Zheng X, Ibrahim YM, Wilkins CS, Renslow RS, Thomas DG, Payne SH, Monroe ME, Smith RD, Teeguarden JG, Baker ES, Metz TO. PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association. Bioinformatics (Oxford, England). PMID 28505286 DOI: 10.1093/bioinformatics/btx305  0.72
2017 Deng L, Garimella SVB, Hamid AM, Webb IK, Attah IK, Norheim RV, Prost SA, Zheng X, Sandoval JA, Baker ES, Ibrahim YM, Smith RD. CRIMP Accumulation and Compression of Billions of Ions for Ion Mobility-MS using Traveling Waves in Structures for Lossless Ion Manipulations. Analytical Chemistry. PMID 28497957 DOI: 10.1021/acs.analchem.7b00189  0.44
2017 Deng L, Webb IK, Garimella SV, Hamid AM, Zheng X, Norheim RV, Prost SA, Anderson GA, Sandoval JA, Baker ES, Ibrahim YM, Smith RD. Serpentine Ultra-long Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations. Analytical Chemistry. PMID 28332832 DOI: 10.1021/acs.analchem.7b00185  0.44
2017 Nielson CM, Wiedrick J, Shen J, Jacobs J, Baker ES, Baraff A, Piehowski P, Lee CG, Baratt A, Petyuk V, McWeeney S, Lim JY, Bauer DC, Lane NE, Cawthon PM, ... Smith RD, et al. Identification of Hip BMD Loss and Fracture Risk Markers through Population-based Serum Proteomics. Journal of Bone and Mineral Research : the Official Journal of the American Society For Bone and Mineral Research. PMID 28316103 DOI: 10.1002/jbmr.3125  0.44
2017 Zheng X, Wojcik R, Zhang X, Ibrahim YM, Burnum-Johnson KE, Orton DJ, Monroe ME, Moore RJ, Smith RD, Baker ES. Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry for Enhanced Multidimensional Biological and Environmental Analyses. Annual Review of Analytical Chemistry (Palo Alto, Calif.). PMID 28301728 DOI: 10.1146/annurev-anchem-061516-045212  0.48
2017 Zheng X, Renslow RS, Makola MM, Webb IK, Deng L, Thomas DG, Govind N, Ibrahim YM, Kabanda MM, Dubery IA, Heyman HM, Smith RD, Madala NE, Baker ES. Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry. The Journal of Physical Chemistry Letters. PMID 28267339 DOI: 10.1021/acs.jpclett.6b03015  0.44
2017 Ibrahim YM, Hamid AM, Deng L, Garimella SV, Webb IK, Baker ES, Smith RD. New frontiers for mass spectrometry based upon structures for lossless ion manipulations. The Analyst. PMID 28262893 DOI: 10.1039/c7an00031f  0.44
2017 Liberton M, Chrisler WB, Nicora CD, Moore RJ, Smith RD, Koppenaal DW, Pakrasi HB, Jacobs JM. Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803. Plos One. 12: e0173251. PMID 28253354 DOI: 10.1371/journal.pone.0173251  0.36
2017 Ibrahim YM, Hamid AM, Cox JT, Garimella SV, Smith RD. Ion Elevators and Escalators in Multilevel Structures for Lossless Ion Manipulations. Analytical Chemistry. 89: 1972-1977. PMID 28208272 DOI: 10.1021/acs.analchem.6b04500  0.4
2017 Kyle JE, Crowell KL, Casey CP, Fujimoto GM, Kim S, Dautel SE, Smith RD, Payne SH, Metz TO. LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. Bioinformatics (Oxford, England). PMID 28158427 DOI: 10.1093/bioinformatics/btx046  0.72
2017 Wojcik R, Webb IK, Deng L, Garimella SV, Prost SA, Ibrahim YM, Baker ES, Smith RD. Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations. International Journal of Molecular Sciences. 18. PMID 28106768 DOI: 10.3390/ijms18010183  0.44
2017 Burnum-Johnson KE, Kyle JE, Eisfeld AJ, Casey CP, Stratton KG, Gonzalez JF, Habyarimana F, Negretti NM, Sims AC, Chauhan S, Thackray LB, Halfmann PJ, Walters KB, Kim YM, Zink EM, ... ... Smith RD, et al. MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. The Analyst. PMID 28091625 DOI: 10.1039/c6an02486f  0.72
2017 Shen Y, Tolić N, Piehowski PD, Shukla AK, Kim S, Zhao R, Qu Y, Robinson E, Smith RD, Paša-Tolić L. High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics. Journal of Chromatography. A. PMID 28077236 DOI: 10.1016/j.chroma.2017.01.008  0.32
2017 Metz TO, Baker ES, Schymanski EL, Renslow RS, Thomas DG, Causon TJ, Webb IK, Hann S, Smith RD, Teeguarden JG. Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go? Bioanalysis. 9: 81-98. PMID 27921453 DOI: 10.4155/bio-2016-0244  0.72
2016 Zhang X, Romm M, Zheng X, Zink EM, Kim YM, Burnum-Johnson KE, Orton DJ, Apffel A, Ibrahim YM, Monroe ME, Moore RJ, Smith JN, Ma J, Renslow RS, Thomas DG, ... ... Smith RD, et al. SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids. Clinical Mass Spectrometry (Del Mar, Calif.). 2: 1-10. PMID 29276770 DOI: 10.1016/j.clinms.2016.11.002  0.72
2016 Deng L, Ibrahim YM, Baker ES, Aly NA, Hamid AM, Zhang X, Zheng X, Garimella SVB, Webb IK, Prost SA, Sandoval JA, Norheim RV, Anderson GA, Tolmachev AV, Smith RD. Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry. Chemistryselect. 1: 2396-2399. PMID 28936476 DOI: 10.1002/slct.201600460  0.52
2016 Ibrahim YM, Garimella SV, Prost SA, Wojcik R, Norheim RV, Baker ES, Rusyn I, Smith RD. Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform. Analytical Chemistry. 88: 12152-12160. PMID 28193022 DOI: 10.1021/acs.analchem.6b03027  0.44
2016 Ahmad R, Nicora CD, Shukla AK, Smith RD, Qian WJ, Liu AY. An efficient method for native protein purification in the selected range from prostate cancer tissue digests. Chinese Clinical Oncology. 5: 78. PMID 28061542 DOI: 10.21037/cco.2016.12.03  0.32
2016 Clair G, Piehowski PD, Nicola T, Kitzmiller JA, Huang EL, Zink EM, Sontag RL, Orton DJ, Moore RJ, Carson JP, Smith RD, Whitsett JA, Corley RA, Ambalavanan N, Ansong C. Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples. Scientific Reports. 6: 39223. PMID 28004771 DOI: 10.1038/srep39223  0.48
2016 Madar IH, Ko SI, Kim H, Mun DG, Kim S, Smith RD, Lee SW. Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to increase sensitivity and accuracy in peptide identifications from tandem mass spectra of co-fragmentation. Analytical Chemistry. PMID 27966901 DOI: 10.1021/acs.analchem.6b03874  0.32
2016 Kyle JE, Casey CP, Stratton KG, Zink EM, Kim YM, Zheng X, Monroe ME, Weitz KK, Bloodsworth KJ, Orton DJ, Ibrahim YM, Moore RJ, Lee CG, Pedersen C, Orwoll E, ... Smith RD, et al. Comparing Identified and Statistically Significant Lipids and Polar Metabolites in 15-Year Old Serum and Dried Blood Spot Samples for Longitudinal Studies. Rapid Communications in Mass Spectrometry : Rcm. PMID 27958645 DOI: 10.1002/rcm.7808  0.48
2016 Garimella SV, Hamid AM, Deng L, Ibrahim YM, Webb IK, Baker ES, Prost SA, Norheim RV, Anderson GA, Smith RD. 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: 11877-11885. PMID 27934097 DOI: 10.1021/acs.analchem.6b03660  0.44
2016 Smith DP, Nicora CD, Carini P, Lipton MS, Norbeck AD, Smith RD, Giovannoni SJ. Proteome Remodeling in Response to Sulfur Limitation in "Candidatus Pelagibacter ubique". Msystems. 1. PMID 27822545 DOI: 10.1128/mSystems.00068-16  0.36
2016 Nakayasu ES, Nicora CD, Sims AC, Burnum-Johnson KE, Kim YM, Kyle JE, Matzke MM, Shukla AK, Chu RK, Schepmoes AA, Jacobs JM, Baric RS, Webb-Robertson BJ, Smith RD, Metz TO. MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses. Msystems. 1. PMID 27822525 DOI: 10.1128/mSystems.00043-16  0.72
2016 Deng L, Ibrahim YM, Garimella SV, Webb IK, Hamid AM, Norheim RV, Prost SA, Sandoval JA, Baker ES, Smith RD. Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations. Analytical Chemistry. PMID 27715008 DOI: 10.1021/acs.analchem.6b02678  0.44
2016 Khadempour L, Burnum-Johnson KE, Baker ES, Nicora CD, Webb-Robertson BM, White RA, Monroe ME, Huang EL, Smith RD, Currie CR. The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates. Molecular Ecology. PMID 27696597 DOI: 10.1111/mec.13872  0.44
2016 Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AW, et al. Corrigendum: The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nature Microbiology. 1: 16210. PMID 27694837 DOI: 10.1038/nmicrobiol.2016.210  0.36
2016 Burnum-Johnson KE, Nie S, Casey CP, Monroe ME, Orton DJ, Ibrahim YM, Gritsenko MA, Clauss TR, Shukla AK, Moore RJ, Purvine SO, Shi T, Qian W, Liu T, Baker ES, ... Smith RD, et al. Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry. Molecular & Cellular Proteomics : McP. PMID 27670688 DOI: 10.1074/mcp.M116.061143  0.48
2016 Dhondt I, Petyuk VA, Cai H, Vandemeulebroucke L, Vierstraete A, Smith RD, Depuydt G, Braeckman BP. FOXO/DAF-16 Activation Slows Down Turnover of the Majority of Proteins in C. elegans. Cell Reports. 16: 3028-3040. PMID 27626670 DOI: 10.1016/j.celrep.2016.07.088  0.72
2016 Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, Bruemmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes. Elife. 5. PMID 27623010 DOI: 10.7554/eLife.15614  0.72
2016 Zheng X, Zhang X, Schocker NS, Renslow RS, Orton DJ, Khamsi J, Ashmus RA, Almeida IC, Tang K, Costello CE, Smith RD, Michael K, Baker ES. Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses. Analytical and Bioanalytical Chemistry. PMID 27604268 DOI: 10.1007/s00216-016-9866-4  0.72
2016 Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AW, et al. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nature Microbiology. 1: 16065. PMID 27573103 DOI: 10.1038/nmicrobiol.2016.65  0.72
2016 Deng L, Ibrahim YM, Hamid AM, Garimella SV, Webb IK, Zheng X, Prost SA, Sandoval JA, Norheim RV, Anderson GA, Tolmachev AV, Baker ES, Smith RD. Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13-m Serpentine Path Length Structures for Lossless Ion Manipulations Module. Analytical Chemistry. PMID 27531027 DOI: 10.1021/acs.analchem.6b01915  0.72
2016 Hamid AM, Garimella SV, Ibrahim YM, Deng L, Zheng X, Webb IK, Anderson GA, Prost SA, Norheim RV, Tolmachev AV, Baker ES, Smith RD. Achieving high resolution ion mobility separations using traveling waves in compact multi-turn Structures for Lossless Ion Manipulations. Analytical Chemistry. PMID 27479234 DOI: 10.1021/acs.analchem.6b01914  0.72
2016 Waltman PH, Guo J, Reistetter EN, Purvine S, Ansong CK, van Baren MJ, Wong CH, Wei CL, Smith RD, Callister SJ, Stuart JM, Worden AZ. Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. Plos One. 11: e0155839. PMID 27434306 DOI: 10.1371/journal.pone.0155839  0.72
2016 Shi T, Niepel M, McDermott JE, Gao Y, Nicora CD, Chrisler WB, Markillie LM, Petyuk VA, Smith RD, Rodland KD, Sorger PK, Qian WJ, Wiley HS. Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway. Science Signaling. 9: rs6. PMID 27405981 DOI: 10.1126/scisignal.aaf0891  0.72
2016 Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, ... ... Smith RD, et al. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. PMID 27372738 DOI: 10.1016/j.cell.2016.05.069  0.72
2016 Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics. PMID 27302376 DOI: 10.1002/pmic.201500449  0.72
2016 Sigdel TK, Gao Y, He J, Wang A, Nicora CD, Fillmore TL, Shi T, Webb-Robertson BJ, Smith RD, Qian WJ, Salvatierra O, Camp DG, Sarwal MM. Mining the human urine proteome for monitoring renal transplant injury. Kidney International. PMID 27165815 DOI: 10.1016/j.kint.2015.12.049  0.72
2016 Webb IK, Garimella SV, Norheim RV, Baker ES, Ibrahim YM, Smith RD. A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation. Journal of the American Society For Mass Spectrometry. PMID 27098413 DOI: 10.1007/s13361-016-1397-x  0.72
2016 Liberton M, Saha R, Jacobs JM, Nguyen AY, Gritsenko MA, Smith RD, Koppenaal DW, Pakrasi HB. Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium. Molecular & Cellular Proteomics : McP. PMID 27056914 DOI: 10.1074/mcp.M115.057240  0.72
2016 Garimella SV, Ibrahim YM, Tang K, Webb IK, Baker ES, Tolmachev AV, Chen TC, Anderson GA, Smith RD. Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry. Journal of the American Society For Mass Spectrometry. PMID 27052738 DOI: 10.1007/s13361-016-1371-7  0.72
2016 Nielson CM, Jones KS, Chun RF, Jacobs JM, Wang Y, Hewison M, Adams JS, Swanson CM, Lee CG, Vanderschueren D, Pauwels S, Prentice A, Smith RD, Shi T, Gao Y, et al. Free 25-hydroxyvitamin D: impact of vitamin D binding protein assays on racial-genotypic associations. The Journal of Clinical Endocrinology and Metabolism. jc20161104. PMID 27007693 DOI: 10.1210/jc.2016-1104  0.72
2016 Liu R, Chen S, Baker ES, Smith RD, Zeng XC, Gong B. Correction: Surprising impact of remote groups on the folding-unfolding and dimer-chain equilibria of bifunctional H-bonding unimers. Chemical Communications (Cambridge, England). PMID 27003741 DOI: 10.1039/c6cc90142e  0.44
2016 Chan CY, Gritsenko MA, Smith RD, Qian WJ. The current state of the art of quantitative phosphoproteomics and its applications to diabetes research. Expert Review of Proteomics. PMID 26960075 DOI: 10.1586/14789450.2016.1164604  0.72
2016 Wu C, Duan J, Liu T, Smith RD, Qian WJ. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. PMID 26868616 DOI: 10.1016/j.jchromb.2016.01.015  0.72
2016 Gritsenko MA, Xu Z, Liu T, Smith RD. Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS. Methods in Molecular Biology (Clifton, N.J.). 1410: 237-47. PMID 26867748 DOI: 10.1007/978-1-4939-3524-6_14  0.72
2016 Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, ... ... Smith RD, et al. Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays. Methods in Molecular Biology (Clifton, N.J.). 1410: 223-36. PMID 26867747 DOI: 10.1007/978-1-4939-3524-6_13  0.72
2016 Tisoncik-Go J, Gasper DJ, Kyle JE, Eisfeld AJ, Selinger C, Hatta M, Morrison J, Korth MJ, Zink EM, Kim YM, Schepmoes AA, Nicora CD, Purvine SO, Weitz KK, Peng X, ... ... Smith RD, et al. Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism. Cell Host & Microbe. 19: 254-66. PMID 26867183 DOI: 10.1016/j.chom.2016.01.002  0.72
2016 Liu R, Cheng S, Baker ES, Smith RD, Zeng XC, Gong B. Surprising impact of remote groups on the folding-unfolding and dimer-chain equilibria of bifunctional H-bonding unimers. Chemical Communications (Cambridge, England). PMID 26830456 DOI: 10.1039/c6cc00224b  0.72
2016 Kyle JE, Zhang X, Weitz KK, Monroe ME, Ibrahim YM, Moore RJ, Cha J, Sun X, Lovelace ES, Wagoner J, Polyak SJ, Metz TO, Dey SK, Smith RD, Burnum-Johnson KE, et al. Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. The Analyst. PMID 26734689 DOI: 10.1039/c5an02062j  0.4
2016 Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, ... ... Smith RD, et al. Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clinical Chemistry. 62: 48-69. PMID 26719571 DOI: 10.1373/clinchem.2015.250563  0.32
2015 El Ouaamari A, Dirice E, Gedeon N, Hu J, Zhou JY, Shirakawa J, Hou L, Goodman J, Karampelias C, Qiang G, Boucher J, Martinez R, Gritsenko MA, De Jesus DF, Kahraman S, ... ... Smith RD, et al. SerpinB1 Promotes Pancreatic β Cell Proliferation. Cell Metabolism. PMID 26701651 DOI: 10.1016/j.cmet.2015.12.001  0.72
2015 Duan J, Kodali VK, Gaffrey MJ, Guo J, Chu RK, Camp DG, Smith RD, Thrall BD, Qian WJ. Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function during Nanoparticle-Induced Oxidative Stress. Acs Nano. PMID 26700264 DOI: 10.1021/acsnano.5b05524  0.72
2015 Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, ... ... Smith RD, et al. Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts. Journal of Proteome Research. PMID 26653538 DOI: 10.1021/acs.jproteome.5b00859  0.4
2015 Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, ... ... Smith RD, et al. An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer. Molecular & Cellular Proteomics : McP. PMID 26631509 DOI: 10.1074/mcp.M115.056226  0.72
2015 Burnet MC, Dohnalkova AC, Neumann AP, Lipton MS, Smith RD, Suen G, Callister SJ. Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85. Plos One. 10: e0143809. PMID 26629814 DOI: 10.1371/journal.pone.0143809  0.72
2015 Wang H, Shi T, Qian WJ, Liu T, Kagan J, Srivastava S, Smith RD, Rodland KD, Camp DG. The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification. Expert Review of Proteomics. PMID 26581546 DOI: 10.1586/14789450.2016.1122529  0.72
2015 Lin TY, Anderson GA, Norheim RV, Prost SA, LaMarche BL, Leach FE, Auberry KJ, Smith RD, Koppenaal DW, Robinson EW, Paša-Tolić L. An adaptable multiple power source for mass spectrometry and other scientific instruments. The Review of Scientific Instruments. 86: 094102. PMID 26429459 DOI: 10.1063/1.4930967  0.72
2015 Aylward FO, Khadempour L, Tremmel DM, McDonald BR, Nicora CD, Wu S, Moore RJ, Orton DJ, Monroe ME, Piehowski PD, Purvine SO, Smith RD, Lipton MS, Burnum-Johnson KE, Currie CR. Correction: 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: e0139151. PMID 26398520 DOI: 10.1371/journal.pone.0139151  0.48
2015 Aylward FO, Khadempour L, Tremmel DM, McDonald BR, Nicora CD, Wu S, Moore RJ, Orton DJ, Monroe ME, Piehowski PD, Purvine SO, Smith RD, Lipton MS, Burnum-Johnson KE, Currie CR. 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: e0134752. PMID 26317212 DOI: 10.1371/journal.pone.0134752  0.72
2015 Payne SH, Monroe ME, Overall CC, Kiebel GR, Degan M, Gibbons BC, Fujimoto GM, Purvine SO, Adkins JN, Lipton MS, Smith RD. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. Scientific Data. 2: 150041. PMID 26306205 DOI: 10.1038/sdata.2015.41  0.72
2015 Bhatt S, Gupta MK, Khamaisi M, Martinez R, Gritsenko MA, Wagner BK, Guye P, Busskamp V, Shirakawa J, Wu G, Liew CW, Clauss TR, Valdez I, El Ouaamari A, Dirice E, ... ... Smith RD, et al. Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes. Cell Metabolism. 22: 239-52. PMID 26244933 DOI: 10.1016/j.cmet.2015.07.015  0.32
2015 Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold RH, Smith RD, Noble WS, MacCoss MJ. Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Molecular & Cellular Proteomics : McP. PMID 26217018 DOI: 10.1074/mcp.O114.047035  0.72
2015 El Ouaamari A, Zhou J, Liew CW, Shirakawa J, Dirice E, Gedeon N, Kahraman S, De Jesus DF, Bhatt S, Kim JS, Clauss TR, Camp DG, Smith RD, Qian WJ, Kulkarni RN. Compensatory Islet Response to Insulin Resistance Revealed by Quantitative Proteomics. Journal of Proteome Research. PMID 26151086 DOI: 10.1021/acs.jproteome.5b00587  0.72
2015 Nakayasu ES, Sydor MA, Brown RN, Sontag RL, Sobreira TJ, Slysz GW, Humphrys DR, Skarina T, Onoprienko O, Di Leo R, Kaiser BL, Li J, Ansong C, Cambronne ED, Smith RD, et al. Identification of Salmonella Typhimurium deubiquitinase SseL substrates by immunoaffinity enrichment and quantitative proteomic analysis. Journal of Proteome Research. PMID 26147956 DOI: 10.1021/acs.jproteome.5b00574  0.72
2015 Zhang X, Ibrahim YM, Chen TC, Kyle JE, Norheim RV, Monroe ME, Smith RD, Baker ES. Enhancing biological analyses with three dimensional field asymmetric ion mobility, low field drift tube ion mobility and mass spectrometry (μFAIMS/IMS-MS) separations. The Analyst. PMID 26140287 DOI: 10.1039/c5an00897b  0.72
2015 Vrablik TL, Petyuk VA, Larson EM, Smith RD, Watts JL. Lipidomic and proteomic analysis of Caenorhabditis elegans lipid droplets and identification of ACS-4 as a lipid droplet-associated protein. Biochimica Et Biophysica Acta. PMID 26121959 DOI: 10.1016/j.bbalip.2015.06.004  0.72
2015 Kebaabetswe LP, Haick AK, Gritsenko MA, Fillmore TL, Chu RK, Purvine SO, Webb-Robertson BJ, Matzke MM, Smith RD, Waters KM, Metz TO, Miura TA. Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus. Virology. 483: 96-107. PMID 25965799 DOI: 10.1016/j.virol.2015.03.045  0.72
2015 Webb-Robertson BJ, Wiberg HK, Matzke MM, Brown JN, Wang J, McDermott JE, Smith RD, Rodland KD, Metz TO, Pounds JG, Waters KM. Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics. Journal of Proteome Research. 14: 1993-2001. PMID 25855118 DOI: 10.1021/pr501138h  0.72
2015 Yu J, Liberton M, Cliften PF, Head RD, Jacobs JM, Smith RD, Koppenaal DW, Brand JJ, Pakrasi HB. Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO₂. Scientific Reports. 5: 8132. PMID 25633131 DOI: 10.1038/srep08132  0.72
2015 Chen Y, Leach FE, Kaiser NK, Dang X, Ibrahim YM, Norheim RV, Anderson GA, Smith RD, Marshall AG. Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer. Journal of Mass Spectrometry : Jms. 50: 280-4. PMID 25601704 DOI: 10.1002/jms.3523  0.72
2015 Shi T, Gao Y, Gaffrey MJ, Nicora CD, Fillmore TL, Chrisler WB, Gritsenko MA, Wu C, He J, Bloodsworth KJ, Zhao R, Camp DG, Liu T, Rodland KD, Smith RD, et al. Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment. Analytical Chemistry. 87: 1103-10. PMID 25517423 DOI: 10.1021/ac503797x  0.72
2015 Merkley ED, Wrighton KC, Castelle CJ, Anderson BJ, Wilkins MJ, Shah V, Arbour T, Brown JN, Singer SW, Smith RD, Lipton MS. Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis. Journal of Proteome Research. 14: 1361-75. PMID 25496566 DOI: 10.1021/pr500983v  0.72
2015 Chen TC, Webb IK, Prost SA, Harrer MB, Norheim RV, Tang K, Ibrahim YM, Smith RD. Rectangular ion funnel: a new ion funnel interface for structures for lossless ion manipulations. Analytical Chemistry. 87: 716-22. PMID 25409343 DOI: 10.1021/ac503564c  0.72
2015 Cox JT, Marginean I, Smith RD, Tang K. On the ionization and ion transmission efficiencies of different ESI-MS interfaces. Journal of the American Society For Mass Spectrometry. 26: 55-62. PMID 25267087 DOI: 10.1007/s13361-014-0998-5  0.72
2015 Bhatt S, Gupta MK, Khamaisi M, Martinez R, Gritsenko MA, Wagner BK, Guye P, Busskamp V, Shirakawa J, Wu G, Liew CW, Clauss TR, Valdez I, El Ouaamari A, Dirice E, ... ... Smith RD, et al. Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes Cell Metabolism. 22: 239-252. DOI: 10.1016/j.cmet.2015.07.015  0.72
2015 Wu C, Liu T, Baker ES, Rodland KD, Smith RD. Mass spectrometry for biomarker development General Methods in Biomarker Research and Their Applications. 1: 17-48. DOI: 10.1007/978-94-007-7696-8_21  0.72
2014 Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, ... ... Smith RD, et al. A comprehensive collection of systems biology data characterizing the host response to viral infection. Scientific Data. 1: 140033. PMID 25977790 DOI: 10.1038/sdata.2014.33  0.72
2014 Sigdel TK, Ng YW, Lee S, Nicora CD, Qian WJ, Smith RD, Camp DG, Sarwal MM. Perturbations in the urinary exosome in transplant rejection. Frontiers in Medicine. 1: 57. PMID 25593928 DOI: 10.3389/fmed.2014.00057  0.32
2014 Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM. Bayesian proteoform modeling improves protein quantification of global proteomic measurements. Molecular & Cellular Proteomics : McP. 13: 3639-46. PMID 25433089 DOI: 10.1074/mcp.M113.030932  0.72
2014 Jonkers W, Leeder AC, Ansong C, Wang Y, Yang F, Starr TL, Camp DG, Smith RD, Glass NL. HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa. Plos Genetics. 10: e1004783. PMID 25412208 DOI: 10.1371/journal.pgen.1004783  0.72
2014 Shin AC, Fasshauer M, Filatova N, Grundell LA, Zielinski E, Zhou JY, Scherer T, Lindtner C, White PJ, Lapworth AL, Ilkayeva O, Knippschild U, Wolf AM, Scheja L, Grove KL, ... Smith RD, et al. Brain insulin lowers circulating BCAA levels by inducing hepatic BCAA catabolism. Cell Metabolism. 20: 898-909. PMID 25307860 DOI: 10.1016/j.cmet.2014.09.003  0.72
2014 Brown JN, Brewer HM, Nicora CD, Weitz KK, Morris MJ, Skabelund AJ, Adkins JN, Smith RD, Cho JH, Gelinas R. Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea. Bmc Medical Genomics. 7: 58. PMID 25282157 DOI: 10.1186/1755-8794-7-58  0.72
2014 He J, Sun X, Shi T, Schepmoes AA, Fillmore TL, Petyuk VA, Xie F, Zhao R, Gritsenko MA, Yang F, Kitabayashi N, Chae SS, Rubin MA, Siddiqui J, Wei JT, ... ... Smith RD, et al. Antibody-independent targeted quantification of TMPRSS2-ERG fusion protein products in prostate cancer. Molecular Oncology. 8: 1169-80. PMID 25266362 DOI: 10.1016/j.molonc.2014.02.004  0.72
2014 Woo S, Cha SW, Na S, Guest C, Liu T, Smith RD, Rodland KD, Payne S, Bafna V. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data. Proteomics. 14: 2719-30. PMID 25263569 DOI: 10.1002/pmic.201400206  0.72
2014 Garimella SV, Ibrahim YM, Webb IK, Tolmachev AV, Zhang X, Prost SA, Anderson GA, Smith RD. Simulation of electric potentials and ion motion in planar electrode structures for lossless ion manipulations (SLIM). Journal of the American Society For Mass Spectrometry. 25: 1890-6. PMID 25257188 DOI: 10.1007/s13361-014-0976-y  0.72
2014 Cox JT, Kronewitter SR, Shukla AK, Moore RJ, Smith RD, Tang K. High sensitivity combined with extended structural coverage of labile compounds via nanoelectrospray ionization at subambient pressures. Analytical Chemistry. 86: 9504-11. PMID 25222651 DOI: 10.1021/ac502767y  0.72
2014 Webb IK, Garimella SV, Tolmachev AV, Chen TC, Zhang X, Cox JT, Norheim RV, Prost SA, LaMarche B, Anderson GA, Ibrahim YM, Smith RD. Mobility-resolved ion selection in uniform drift field ion mobility spectrometry/mass spectrometry: dynamic switching in structures for lossless ion manipulations. Analytical Chemistry. 86: 9632-7. PMID 25222548 DOI: 10.1021/ac502139e  0.72
2014 Tolmachev AV, Webb IK, Ibrahim YM, Garimella SV, Zhang X, Anderson GA, Smith RD. Characterization of ion dynamics in structures for lossless ion manipulations. Analytical Chemistry. 86: 9162-8. PMID 25152178 DOI: 10.1021/ac502054p  0.72
2014 Webb IK, Garimella SV, Tolmachev AV, Chen TC, Zhang X, Norheim RV, Prost SA, LaMarche B, Anderson GA, Ibrahim YM, Smith RD. Experimental evaluation and optimization of structures for lossless ion manipulations for ion mobility spectrometry with time-of-flight mass spectrometry. Analytical Chemistry. 86: 9169-76. PMID 25152066 DOI: 10.1021/ac502055e  0.72
2014 Nakayasu ES, Wu S, Sydor MA, Shukla AK, Weitz KK, Moore RJ, Hixson KK, Kim JS, Petyuk VA, Monroe ME, Pasa-Tolic L, Qian WJ, Smith RD, Adkins JN, Ansong C. A method to determine lysine acetylation stoichiometries. International Journal of Proteomics. 2014: 730725. PMID 25143833 DOI: 10.1155/2014/730725  0.48
2014 Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM. Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements. Molecular & Cellular Proteomics : McP. PMID 25129695 DOI: 10.1074/mcp.O113.030932  0.72
2014 Guo J, Nguyen AY, Dai Z, Su D, Gaffrey MJ, Moore RJ, Jacobs JM, Monroe ME, Smith RD, Koppenaal DW, Pakrasi HB, Qian WJ. Proteome-wide light/dark modulation of thiol oxidation in cyanobacteria revealed by quantitative site-specific redox proteomics. Molecular & Cellular Proteomics : McP. 13: 3270-85. PMID 25118246 DOI: 10.1074/mcp.M114.041160  0.72
2014 Ansong C, Sadler NC, Hill EA, Lewis MP, Zink EM, Smith RD, Beliaev AS, Konopka AE, Wright AT. Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria. Frontiers in Microbiology. 5: 325. PMID 25071738 DOI: 10.3389/fmicb.2014.00325  0.72
2014 Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, et al. Proteogenomic characterization of human colon and rectal cancer. Nature. 513: 382-7. PMID 25043054 DOI: 10.1038/nature13438  0.72
2014 Huang EL, Aylward FO, Kim YM, Webb-Robertson BJ, Nicora CD, Hu Z, Metz TO, Lipton MS, Smith RD, Currie CR, Burnum-Johnson KE. The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation. Environmental Microbiology Reports. 6: 389-95. PMID 24992538 DOI: 10.1111/1758-2229.12163  0.72
2014 Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Rodriguez H, Paulovich AG. CPTAC Assay Portal: a repository of targeted proteomic assays. Nature Methods. 11: 703-4. PMID 24972168 DOI: 10.1038/nmeth.3002  0.72
2014 Ryu SY, Qian WJ, Camp DG, Smith RD, Tompkins RG, Davis RW, Xiao W. Detecting differential protein expression in large-scale population proteomics. Bioinformatics (Oxford, England). 30: 2741-6. PMID 24928210 DOI: 10.1093/bioinformatics/btu341  0.72
2014 Xiong Y, Coradetti ST, Li X, Gritsenko MA, Clauss T, Petyuk V, Camp D, Smith R, Cate JH, Yang F, Glass NL. The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation. Fungal Genetics and Biology : Fg & B. 72: 21-33. PMID 24881580 DOI: 10.1016/j.fgb.2014.05.005  0.72
2014 Aryal UK, Callister SJ, McMahon BH, McCue LA, Brown J, Stöckel J, Liberton M, Mishra S, Zhang X, Nicora CD, Angel TE, Koppenaal DW, Smith RD, Pakrasi HB, Sherman LA. Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece. Journal of Proteome Research. 13: 3262-76. PMID 24846609 DOI: 10.1021/pr5000889  0.72
2014 Menachery VD, Eisfeld AJ, Schäfer A, Josset L, Sims AC, Proll S, Fan S, Li C, Neumann G, Tilton SC, Chang J, Gralinski LE, Long C, Green R, Williams CM, ... ... Smith RD, et al. Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses. Mbio. 5: e01174-14. PMID 24846384 DOI: 10.1128/mBio.01174-14  0.72
2014 Prost SA, Crowell KL, Baker ES, Ibrahim YM, Clowers BH, Monroe ME, Anderson GA, Smith RD, Payne SH. Detecting and removing data artifacts in Hadamard transform ion mobility-mass spectrometry measurements. Journal of the American Society For Mass Spectrometry. 25: 2020-7. PMID 24796262 DOI: 10.1007/s13361-014-0895-y  0.72
2014 Ibrahim YM, Garimella SV, Tolmachev AV, Baker ES, Smith RD. Improving ion mobility measurement sensitivity by utilizing helium in an ion funnel trap. Analytical Chemistry. 86: 5295-9. PMID 24786390 DOI: 10.1021/ac404250z  0.72
2014 Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SR, ... ... Smith RD, et al. Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Molecular & Cellular Proteomics : McP. 13: 1690-704. PMID 24719451 DOI: 10.1074/mcp.M113.036392  0.72
2014 Dominy SS, Brown JN, Ryder MI, Gritsenko M, Jacobs JM, Smith RD. Proteomic analysis of saliva in HIV-positive heroin addicts reveals proteins correlated with cognition. Plos One. 9: e89366. PMID 24717448 DOI: 10.1371/journal.pone.0089366  0.72
2014 Malouli D, Hansen SG, Nakayasu ES, Marshall EE, Hughes CM, Ventura AB, Gilbride RM, Lewis MS, Xu G, Kreklywich C, Whizin N, Fischer M, Legasse AW, Viswanathan K, Siess D, ... ... Smith RD, et al. Cytomegalovirus pp65 limits dissemination but is dispensable for persistence. The Journal of Clinical Investigation. 124: 1928-44. PMID 24691437 DOI: 10.1172/JCI67420  0.72
2014 Smith JS, Angel TE, Chavkin C, Orton DJ, Moore RJ, Smith RD. Characterization of individual mouse cerebrospinal fluid proteomes. Proteomics. 14: 1102-6. PMID 24677814 DOI: 10.1002/pmic.201300241  0.72
2014 Cox JT, Marginean I, Kelly RT, Smith RD, Tang K. Improving the sensitivity of mass spectrometry by using a new sheath flow electrospray emitter array at subambient pressures. Journal of the American Society For Mass Spectrometry. 25: 2028-37. PMID 24676894 DOI: 10.1007/s13361-014-0856-5  0.72
2014 Zhang Q, Matzke M, Schepmoes AA, Moore RJ, Webb-Robertson BJ, Hu Z, Monroe ME, Qian WJ, Smith RD, Morgan WF. High and low doses of ionizing radiation induce different secretome profiles in a human skin model. Plos One. 9: e92332. PMID 24642900 DOI: 10.1371/journal.pone.0092332  0.72
2014 Smith RD. Honoring Dr. Jean H. Futrell. Journal of the American Society For Mass Spectrometry. 25: 699-701. PMID 24627182 DOI: 10.1007/s13361-014-0829-8  0.72
2014 Amidan BG, Orton DJ, Lamarche BL, Monroe ME, Moore RJ, Venzin AM, Smith RD, Sego LH, Tardiff MF, Payne SH. Signatures for mass spectrometry data quality. Journal of Proteome Research. 13: 2215-22. PMID 24611607 DOI: 10.1021/pr401143e  0.72
2014 Wu S, Brown JN, Tolić N, Meng D, Liu X, Zhang H, Zhao R, Moore RJ, Pevzner P, Smith RD, Paša-Tolić L. Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry. Proteomics. 14: 1211-22. PMID 24591407 DOI: 10.1002/pmic.201300378  0.72
2014 Martin JL, Yates PA, Soysa R, Alfaro JF, Yang F, Burnum-Johnson KE, Petyuk VA, Weitz KK, Camp DG, Smith RD, Wilmarth PA, David LL, Ramasamy G, Myler PJ, Carter NS. Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani. Plos Pathogens. 10: e1003938. PMID 24586154 DOI: 10.1371/journal.ppat.1003938  0.72
2014 Depuydt G, Xie F, Petyuk VA, Smolders A, Brewer HM, Camp DG, Smith RD, Braeckman BP. LC-MS proteomics analysis of the insulin/IGF-1-deficient Caenorhabditis elegans daf-2(e1370) mutant reveals extensive restructuring of intermediary metabolism. Journal of Proteome Research. 13: 1938-56. PMID 24555535 DOI: 10.1021/pr401081b  0.72
2014 Wiedner SD, Anderson LN, Sadler NC, Chrisler WB, Kodali VK, Smith RD, Wright AT. Organelle-specific activity-based protein profiling in living cells. Angewandte Chemie (International Ed. in English). 53: 2919-22. PMID 24505022 DOI: 10.1002/anie.201309135  0.72
2014 Webb IK, Chen TC, Danielson WF, Ibrahim YM, Tang K, Anderson GA, Smith RD. Implementation of dipolar resonant excitation for collision induced dissociation with ion mobility/time-of-flight MS. Journal of the American Society For Mass Spectrometry. 25: 563-71. PMID 24470195 DOI: 10.1007/s13361-013-0815-6  0.72
2014 Slysz GW, Steinke L, Ward DM, Klatt CG, Clauss TR, Purvine SO, Payne SH, Anderson GA, Smith RD, Lipton MS. Automated data extraction from in situ protein-stable isotope probing studies. Journal of Proteome Research. 13: 1200-10. PMID 24467184 DOI: 10.1021/pr400633j  0.72
2014 Shvartsburg AA, Ibrahim YM, Smith RD. Differential ion mobility separations in up to 100% helium using microchips. Journal of the American Society For Mass Spectrometry. 25: 480-9. PMID 24402673 DOI: 10.1007/s13361-013-0797-4  0.72
2014 Granholm V, Kim S, Navarro JC, Sjölund E, Smith RD, Käll L. Fast and accurate database searches with MS-GF+Percolator. Journal of Proteome Research. 13: 890-7. PMID 24344789 DOI: 10.1021/pr400937n  0.72
2014 Guo J, Gaffrey MJ, Su D, Liu T, Camp DG, Smith RD, Qian WJ. Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications. Nature Protocols. 9: 64-75. PMID 24336471 DOI: 10.1038/nprot.2013.161  0.72
2014 Sigdel TK, Salomonis N, Nicora CD, Ryu S, He J, Dinh V, Orton DJ, Moore RJ, Hsieh SC, Dai H, Thien-Vu M, Xiao W, Smith RD, Qian WJ, Camp DG, et al. The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics. Molecular & Cellular Proteomics : McP. 13: 621-31. PMID 24335474 DOI: 10.1074/mcp.M113.030577  0.72
2014 Su D, Gaffrey MJ, Guo J, Hatchell KE, Chu RK, Clauss TR, Aldrich JT, Wu S, Purvine S, Camp DG, Smith RD, Thrall BD, Qian WJ. Proteomic identification and quantification of S-glutathionylation in mouse macrophages using resin-assisted enrichment and isobaric labeling. Free Radical Biology & Medicine. 67: 460-70. PMID 24333276 DOI: 10.1016/j.freeradbiomed.2013.12.004  0.72
2014 Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH. Accounting for population variation in targeted proteomics. Journal of Proteome Research. 13: 321-3. PMID 24320210 DOI: 10.1021/pr4011052  0.72
2014 Zaborin A, Defazio JR, Kade M, Kaiser BL, Belogortseva N, Camp DG, Smith RD, Adkins JN, Kim SM, Alverdy A, Goldfeld D, Firestone MA, Collier JH, Jabri B, Tirrell M, et al. Phosphate-containing polyethylene glycol polymers prevent lethal sepsis by multidrug-resistant pathogens. Antimicrobial Agents and Chemotherapy. 58: 966-77. PMID 24277029 DOI: 10.1128/AAC.02183-13  0.72
2014 Shi T, Gao Y, Quek SI, Fillmore TL, Nicora CD, Su D, Zhao R, Kagan J, Srivastava S, Rodland KD, Liu T, Smith RD, Chan DW, Camp DG, Liu AY, et al. A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum. Journal of Proteome Research. 13: 875-82. PMID 24251762 DOI: 10.1021/pr400912c  0.72
2014 Sadler NC, Melnicki MR, Serres MH, Merkley ED, Chrisler WB, Hill EA, Romine MF, Kim S, Zink EM, Datta S, Smith RD, Beliaev AS, Konopka A, Wright AT. Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium. Acs Chemical Biology. 9: 291-300. PMID 24168666 DOI: 10.1021/cb400769v  0.72
2014 Marginean I, Tang K, Smith RD, Kelly RT. Picoelectrospray ionization mass spectrometry using narrow-bore chemically etched emitters. Journal of the American Society For Mass Spectrometry. 25: 30-6. PMID 24122304 DOI: 10.1007/s13361-013-0749-z  0.72
2014 Merkley ED, Metz TO, Smith RD, Baynes JW, Frizzell N. The succinated proteome. Mass Spectrometry Reviews. 33: 98-109. PMID 24115015 DOI: 10.1002/mas.21382  0.72
2013 Smith DP, Thrash JC, Nicora CD, Lipton MS, Burnum-Johnson KE, Carini P, Smith RD, Giovannoni SJ. Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium. Mbio. 4: e00133-12. PMID 24281717 DOI: 10.1128/mBio.00133-12  0.72
2013 Depuydt G, Xie F, Petyuk VA, Shanmugam N, Smolders A, Dhondt I, Brewer HM, Camp DG, Smith RD, Braeckman BP. Reduced insulin/insulin-like growth factor-1 signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans. Molecular & Cellular Proteomics : McP. 12: 3624-39. PMID 24002365 DOI: 10.1074/mcp.M113.027383  0.72
2013 Price RW, Peterson J, Fuchs D, Angel TE, Zetterberg H, Hagberg L, Spudich S, Smith RD, Jacobs JM, Brown JN, Gisslen M. Approach to cerebrospinal fluid (CSF) biomarker discovery and evaluation in HIV infection. Journal of Neuroimmune Pharmacology : the Official Journal of the Society On Neuroimmune Pharmacology. 8: 1147-58. PMID 23943280 DOI: 10.1007/s11481-013-9491-3  0.72
2013 Mitchell HD, Eisfeld AJ, Sims AC, McDermott JE, Matzke MM, Webb-Robertson BJ, Tilton SC, Tchitchek N, Josset L, Li C, Ellis AL, Chang JH, Heegel RA, Luna ML, Schepmoes AA, ... ... Smith RD, et al. A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses. Plos One. 8: e69374. PMID 23935999 DOI: 10.1371/journal.pone.0069374  0.72
2013 Gralinski LE, Bankhead A, Jeng S, Menachery VD, Proll S, Belisle SE, Matzke M, Webb-Robertson BJ, Luna ML, Shukla AK, Ferris MT, Bolles M, Chang J, Aicher L, Waters KM, ... Smith RD, et al. Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury. Mbio. 4. PMID 23919993 DOI: 10.1128/mBio.00271-13  0.72
2013 Tchitchek N, Eisfeld AJ, Tisoncik-Go J, Josset L, Gralinski LE, Bécavin C, Tilton SC, Webb-Robertson BJ, Ferris MT, Totura AL, Li C, Neumann G, Metz TO, Smith RD, Waters KM, et al. Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. Bmc Systems Biology. 7: 69. PMID 23895213 DOI: 10.1186/1752-0509-7-69  0.44
2013 Deatherage Kaiser BL, Li J, Sanford JA, Kim YM, Kronewitter SR, Jones MB, Peterson CT, Peterson SN, Frank BC, Purvine SO, Brown JN, Metz TO, Smith RD, Heffron F, Adkins JN. A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection. Plos One. 8: e67155. PMID 23840608 DOI: 10.1371/journal.pone.0067155  0.72
2013 Aylward FO, Burnum-Johnson KE, Tringe SG, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD, Malfatti SA, Monroe ME, Purvine SO, Goodwin LA, Smith RD, et al. Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Applied and Environmental Microbiology. 79: 3770-8. PMID 23584789 DOI: 10.1128/AEM.03833-12  0.72
2013 Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, et al. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Molecular Biosystems. 9: 1522-34. PMID 23559334 DOI: 10.1039/c3mb25598k  0.72
2013 Piehowski PD, Petyuk VA, Orton DJ, Xie F, Moore RJ, Ramirez-Restrepo M, Engel A, Lieberman AP, Albin RL, Camp DG, Smith RD, Myers AJ. Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis. Journal of Proteome Research. 12: 2128-37. PMID 23495885 DOI: 10.1021/pr301146m  0.72
2013 LaMarche BL, Crowell KL, Jaitly N, Petyuk VA, Shah AR, Polpitiya AD, Sandoval JD, Kiebel GR, Monroe ME, Callister SJ, Metz TO, Anderson GA, Smith RD. MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. Bmc Bioinformatics. 14: 49. PMID 23398735 DOI: 10.1186/1471-2105-14-49  0.44
2013 Sims AC, Tilton SC, Menachery VD, Gralinski LE, Schäfer A, Matzke MM, Webb-Robertson BJ, Chang J, Luna ML, Long CE, Shukla AK, Bankhead AR, Burkett SE, Zornetzer G, Tseng CT, ... ... Smith RD, et al. Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. Journal of Virology. 87: 3885-902. PMID 23365422 DOI: 10.1128/JVI.02520-12  0.72
2013 Piehowski PD, Petyuk VA, Sandoval JD, Burnum KE, Kiebel GR, Monroe ME, Anderson GA, Camp DG, Smith RD. STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results. Proteomics. 13: 766-70. PMID 23303698 DOI: 10.1002/pmic.201200096  0.44
2013 Zhang Q, Fillmore TL, Schepmoes AA, Clauss TR, Gritsenko MA, Mueller PW, Rewers M, Atkinson MA, Smith RD, Metz TO. Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes. The Journal of Experimental Medicine. 210: 191-203. PMID 23277452 DOI: 10.1084/jem.20111843  0.72
2013 Ansong C, Schrimpe-Rutledge AC, Mitchell HD, Chauhan S, Jones MB, Kim YM, McAteer K, Deatherage Kaiser BL, Dubois JL, Brewer HM, Frank BC, McDermott JE, Metz TO, Peterson SN, Smith RD, et al. A multi-omic systems approach to elucidating Yersinia virulence mechanisms. Molecular Biosystems. 9: 44-54. PMID 23147219 DOI: 10.1039/c2mb25287b  0.72
2013 Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, Shukla AK, Smith RD, Waters KM, McDermott JE, Webb-Robertson BJ. A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics. 13: 493-503. PMID 23019139 DOI: 10.1002/pmic.201200269  0.72
2013 Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, ... ... Smith RD, et al. Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling. Current Topics in Microbiology and Immunology. 363: 21-41. PMID 22886542 DOI: 10.1007/82_2012_247  0.72
2012 Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN, Hyduke DR, Adkins JN, Palsson BO. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Molecular Systems Biology. 8: 558. PMID 22735334 DOI: 10.1038/msb.2012.21  0.44
2012 Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO. Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics. Journal of Proteome Research. 11: 3520-32. PMID 22578083 DOI: 10.1021/pr3002996  0.72
2012 Tolmachev AV, Robinson EW, Wu S, Smith RD, Futrell JH, Paša-Toli? L. Angular averaged profiling of the radial electric field in compensated FTICR Cells. Journal of the American Society For Mass Spectrometry. 23: 1169-72. PMID 22565507 DOI: 10.1007/s13361-012-0395-x  0.44
2012 Aylward FO, Burnum KE, Scott JJ, Suen G, Tringe SG, Adams SM, Barry KW, Nicora CD, Piehowski PD, Purvine SO, Starrett GJ, Goodwin LA, Smith RD, Lipton MS, Currie CR. Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. The Isme Journal. 6: 1688-701. PMID 22378535 DOI: 10.1038/ismej.2012.10  0.72
2012 Gao X, Zhang Q, Meng D, Isaac G, Zhao R, Fillmore TL, Chu RK, Zhou J, Tang K, Hu Z, Moore RJ, Smith RD, Katze MG, Metz TO. A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling. Analytical and Bioanalytical Chemistry. 402: 2923-33. PMID 22354571 DOI: 10.1007/s00216-012-5773-5  0.72
2011 Shvartsburg AA, Isaac G, Leveque N, Smith RD, Metz TO. Separation and classification of lipids using differential ion mobility spectrometry. Journal of the American Society For Mass Spectrometry. 22: 1146-55. PMID 21953096 DOI: 10.1007/s13361-011-0114-z  0.72
2011 Rasmussen AL, Diamond DL, McDermott JE, Gao X, Metz TO, Matzke MM, Carter VS, Belisle SE, Korth MJ, Waters KM, Smith RD, Katze MG. Systems virology identifies a mitochondrial fatty acid oxidation enzyme, dodecenoyl coenzyme A delta isomerase, required for hepatitis C virus replication and likely pathogenesis. Journal of Virology. 85: 11646-54. PMID 21917952 DOI: 10.1128/JVI.05605-11  0.44
2011 Kim YM, Metz TO, Hu Z, Wiedner SD, Kim JS, Smith RD, Morgan WF, Zhang Q. Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics. Rapid Communications in Mass Spectrometry : Rcm. 25: 2561-4. PMID 21910289 DOI: 10.1002/rcm.5134  0.72
2010 Shah AR, Davidson J, Monroe ME, Mayampurath AM, Danielson WF, Shi Y, Robinson AC, Clowers BH, Belov ME, Anderson GA, Smith RD. An efficient data format for mass spectrometry-based proteomics. Journal of the American Society For Mass Spectrometry. 21: 1784-8. PMID 20674389 DOI: 10.1016/j.jasms.2010.06.014  0.72
2009 Tolmachev AV, Clowers BH, Belov ME, Smith RD. Coulombic effects in ion mobility spectrometry. Analytical Chemistry. 81: 4778-87. PMID 19438247 DOI: 10.1021/ac900329x  0.72
2008 López-Ferrer D, Petritis K, Lourette NM, Clowers B, Hixson KK, Heibeck T, Prior DC, Pasa-Tolić L, Camp DG, Belov ME, Smith RD. On-line digestion system for protein characterization and proteome analysis. Analytical Chemistry. 80: 8930-6. PMID 19551971 DOI: 10.1021/ac800927v  0.44
2008 Belov ME, Clowers BH, Prior DC, Danielson WF, Liyu AV, Petritis BO, Smith RD. Dynamically multiplexed ion mobility time-of-flight mass spectrometry. Analytical Chemistry. 80: 5873-83. PMID 18582088 DOI: 10.1021/ac8003665  0.72
2008 Clowers BH, Belov ME, Prior DC, Danielson WF, Ibrahim Y, Smith RD. Pseudorandom sequence modifications for ion mobility orthogonal time-of-flight mass spectrometry. Analytical Chemistry. 80: 2464-73. PMID 18311942 DOI: 10.1021/ac7022712  0.72
2008 Clowers BH, Ibrahim YM, Prior DC, Danielson WF, Belov ME, Smith RD. Enhanced ion utilization efficiency using an electrodynamic ion funnel trap as an injection mechanism for ion mobility spectrometry. Analytical Chemistry. 80: 612-23. PMID 18166021 DOI: 10.1021/ac701648p  0.72
2007 Baker ES, Clowers BH, Li F, Tang K, Tolmachev AV, Prior DC, Belov ME, Smith RD. Ion mobility spectrometry-mass spectrometry performance using electrodynamic ion funnels and elevated drift gas pressures. Journal of the American Society For Mass Spectrometry. 18: 1176-87. PMID 17512752 DOI: 10.1016/j.jasms.2007.03.031  0.44
2006 Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology. 24: 1151-61. PMID 16964229 DOI: 10.1038/nbt1239  0.32
1998 Pasa Tolić L, Harms AC, Anderson GA, Smith RD, Willie A, Jorns MS. Electrospray ionization-mass spectrometry characterization of heterotetrameric sarcosine oxidase. Journal of the American Society For Mass Spectrometry. 9: 510-5. PMID 9879365 DOI: 10.1016/S1044-0305(98)00011-7  0.72
1998 Liu C, Tolić LP, Hofstadler SA, Harms AC, Smith RD, Kang C, Sinha N. Probing RegA/RNA interactions using electrospray ionization-fourier transform ion cyclotron resonance-mass spectrometry. Analytical Biochemistry. 262: 67-76. PMID 9735149 DOI: 10.1006/abio.1998.2753  0.72
1998 Wunschel DS, Muddiman DC, Fox KF, Fox A, Smith RD. Heterogeneity in Bacillus cereus PCR products detected by ESI-FTICR mass spectrometry. Analytical Chemistry. 70: 1203-7. PMID 9530010  0.72
1997 Muddiman DC, Anderson GA, Hofstadler SA, Smith RD. Length and base composition of PCR-amplified nucleic acids using mass measurements from electrospray ionization mass spectrometry. Analytical Chemistry. 69: 1543-9. PMID 9109353  0.36
1996 Muddiman DC, Wunschel DS, Liu C, Pasa-Tolić L, Fox KF, Fox A, Anderson GA, Smith RD. Characterization of PCR products from bacilli using electrospray ionization FTICR mass spectrometry. Analytical Chemistry. 68: 3705-12. PMID 8914480  0.72
1996 Liu C, Wu Q, Harms AC, Smith RD. On-line microdialysis sample cleanup for electrospray ionization mass spectrometry of nucleic acid samples. Analytical Chemistry. 68: 3295-9. PMID 8797389 DOI: 10.1021/ac960286j  0.72
1996 Cheng X, Harms AC, Goudreau PN, Terwilliger TC, Smith RD. Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 93: 7022-7. PMID 8692937 DOI: 10.1073/pnas.93.14.7022  0.72
1996 Cheng X, Morin PE, Harms AC, Bruce JE, Ben-David Y, Smith RD. Mass spectrometric characterization of sequence-specific complexes of DNA and transcription factor PU.1 DNA binding domain. Analytical Biochemistry. 239: 35-40. PMID 8660622 DOI: 10.1006/abio.1996.0287  0.72
1996 Wunschel DS, Fox KF, Fox A, Bruce JE, Muddiman DC, Smith RD. Analysis of double-stranded polymerase chain reaction products from the Bacillus cereus group by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Rapid Communications in Mass Spectrometry : Rcm. 10: 29-35. PMID 8563015 DOI: 10.1002/(SICI)1097-0231(19960115)10:1<29::AID-RCM430>3.0.CO;2-#  0.72
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