Richard Dale Smith - Publications

Affiliations: 
Pacific Northwest National Laboratory, Richland, WA, United States 

500 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
2022 Lin A, Piehowski PD, Tsai CF, Makushok T, Yi L, Diaz U, Yan C, Summers D, Sood P, Smith RD, Liu T, Marshall WF. Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells. Current Biology : Cb. PMID 35447087 DOI: 10.1016/j.cub.2022.03.078  0.585
2022 Colby SM, Chang CH, Bade JL, Nunez JR, Blumer MR, Orton DJ, Bloodsworth KJ, Nakayasu ES, Smith RD, Ibrahim YM, Renslow RS, Metz TO. DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data. Analytical Chemistry. 94: 6130-6138. PMID 35430813 DOI: 10.1021/acs.analchem.1c05017  0.325
2022 Woo J, Clair GC, Williams SM, Feng S, Tsai CF, Moore RJ, Chrisler WB, Smith RD, Kelly RT, Paša-Tolić L, Ansong C, Zhu Y. Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering. Cell Systems. PMID 35298923 DOI: 10.1016/j.cels.2022.02.003  0.357
2021 Bilbao A, Gibbons BC, Stow SM, Kyle JE, Bloodsworth KJ, Payne SH, Smith RD, Ibrahim YM, Baker ES, Fjeldsted JC. A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows. Journal of Proteome Research. PMID 34382401 DOI: 10.1021/acs.jproteome.1c00425  0.607
2021 Sims AC, Mitchell HD, Gralinski LE, Kyle JE, Burnum-Johnson KE, Lam M, Fulcher ML, West A, Smith RD, Randell SH, Metz TO, Sheahan TP, Waters KM, Baric RS. Unfolded Protein Response Inhibition Reduces Middle East Respiratory Syndrome Coronavirus-Induced Acute Lung Injury. Mbio. e0157221. PMID 34372702 DOI: 10.1128/mBio.01572-21  0.492
2021 Lee JY, Bilbao A, Conant CR, Bloodsworth KJ, Orton DJ, Zhou M, Wilson JW, Zheng X, Webb IK, Li A, Hixson KK, Fjeldsted JC, Ibrahim YM, Payne SH, Jansson C, ... Smith RD, et al. AutoCCS: Automated collision cross section calculation software for ion mobility spectrometry-mass spectrometry. Bioinformatics (Oxford, England). PMID 34145874 DOI: 10.1093/bioinformatics/btab429  0.603
2021 Jarsberg LG, Kedia K, Wendler J, Wright AT, Piehowski PD, Gritsenko MA, Shi T, Lewinsohn DM, Sigal GB, Weiner MH, Smith RD, Keane J, Jacobs JM, Nahid P. Nutritional markers and proteome in patients undergoing treatment for pulmonary tuberculosis differ by geographic region. Plos One. 16: e0250586. PMID 33951066 DOI: 10.1371/journal.pone.0250586  0.55
2021 Khadempour L, Kyle JE, Webb-Robertson BM, Nicora CD, Smith FB, Smith RD, Lipton MS, Currie CR, Baker ES, Burnum-Johnson KE. From Plants to Ants: Fungal Modification of Leaf Lipids for Nutrition and Communication in the Leaf-Cutter Ant Fungal Garden Ecosystem. Msystems. 6. PMID 33758033 DOI: 10.1128/mSystems.01307-20  0.494
2021 Tsai CF, Smith JS, Eiger DS, Martin K, Liu T, Smith RD, Shi T, Rajagopal S, Jacobs JM. Mass Spectrometry-Based Proteomics for Analysis of Hydrophilic Phosphopeptides. Methods in Molecular Biology (Clifton, N.J.). 2259: 247-257. PMID 33687720 DOI: 10.1007/978-1-0716-1178-4_16  0.315
2020 Orwoll ES, Wiedrick J, Nielson CM, Jacobs J, Baker ES, Piehowski P, Petyuk V, Gao Y, Shi T, Smith RD, Bauer DC, Cummings SR, Lapidus J. Proteomic assessment of serum biomarkers of longevity in older men. Aging Cell. e13253. PMID 33078901 DOI: 10.1111/acel.13253  0.722
2020 Williams SM, Liyu AV, Tsai CF, Moore RJ, Orton DJ, Chrisler WB, Gaffrey MJ, Liu T, Smith RD, Kelly RT, Paša-Tolić L, Zhu Y. Automated Coupling of Nanodroplet Sample Preparation with Liquid Chromatography-Mass Spectrometry for High-Throughput Single-Cell Proteomics. Analytical Chemistry. PMID 32639140 DOI: 10.1021/Acs.Analchem.0C01551  0.37
2020 Hollerbach AL, Li A, Prabhakaran A, Nagy G, Harrilal CP, Conant CR, Norheim RV, Schimelfenig CE, Anderson GA, Garimella SVB, Smith RD, Ibrahim YM. Ultra-High Resolution Ion Mobility Separations Over Extended Path Lengths and Mobility Ranges Achieved using a Multilevel Structures for Lossless Ion Manipulations (SLIM) Module. Analytical Chemistry. PMID 32383592 DOI: 10.1021/Acs.Analchem.0C01397  0.366
2020 Xiang P, Zhu Y, Yang Y, Zhao Z, Williams SM, Moore RJ, Kelly RT, Smith RD, Liu S. Picoflow Liquid Chromatography-Mass Spectrometry for Ultra-sensitive Bottom-up Proteomics using 2-µm i.d. Open Tubular Columns. Analytical Chemistry. PMID 32208662 DOI: 10.1021/Acs.Analchem.9B05639  0.437
2020 Nagy G, Attah IK, Conant CR, Liu W, Garimella SVB, Gunawardena H, Shaw JB, Smith RD, Ibrahim YM. Rapid and Simultaneous Characterization of Drug Conjugation in Heavy and Light Chains of a Monoclonal Antibody Revealed by High-Resolution Ion Mobility Separations in SLIM. Analytical Chemistry. PMID 32142606 DOI: 10.1021/Acs.Analchem.9B05209  0.326
2020 Tsai CF, Zhao R, Williams SM, Moore RJ, Schultz K, Chrisler W, Pasa-Tolic L, Rodland K, Smith RD, Shi T, Zhu Y, Liu T. An improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) strategy for precise quantitative single-cell proteomics. Molecular & Cellular Proteomics : McP. PMID 32127492 DOI: 10.1074/Mcp.Ra119.001857  0.41
2020 Tsai C, Zhao R, Moore R, Williams S, Schultz K, Piehowski P, Pasa-Tolic L, Rodland K, Smith R, Shi T, Zhu Y, Liu T. Abstract 2856: An intelligent boosting to amplify signal with isobaric labeling (iBASIL) strategy for precise quantitative single-cell proteomics analysis Cancer Research. 80: 2856-2856. DOI: 10.1158/1538-7445.Am2020-2856  0.693
2019 Garimella SVB, Nagy G, Ibrahim YM, Smith RD. Opening new paths for biological applications of ion mobility - mass spectrometry using Structures for Lossless Ion Manipulations. Trends in Analytical Chemistry : Trac. 116: 300-307. PMID 32831434 DOI: 10.1016/J.Trac.2019.04.021  0.449
2019 Burnum-Johnson KE, Zheng X, Dodds JN, Ash J, Fourches D, Nicora CD, Wendler JP, Metz TO, Waters KM, Jansson JK, Smith RD, Baker ES. Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples. Trends in Analytical Chemistry : Trac. 116: 292-299. PMID 31798197 DOI: 10.1016/J.Trac.2019.04.022  0.828
2019 Attah I, Nagy G, Garimella SVB, Norheim RV, Anderson GA, Ibrahim YM, Smith RD. Traveling wave-based electrodynamic switch for concurrent dual polarity ion manipulations in Structures for Lossless Ion Manipulations. Analytical Chemistry. PMID 31621288 DOI: 10.1021/Acs.Analchem.9B03987  0.326
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  0.345
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  0.587
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  0.609
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  0.552
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  0.418
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  0.536
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  0.656
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  0.643
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  0.333
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  0.686
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  0.618
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  0.373
2019 Kyle JE, Burnum-Johnson KE, Wendler JP, Eisfeld AJ, Halfmann PJ, Watanabe T, Sahr F, Smith RD, Kawaoka Y, Waters KM, Metz TO. Plasma lipidome reveals critical illness and recovery from human Ebola virus disease. Proceedings of the National Academy of Sciences of the United States of America. 116: 3919-3928. PMID 30808769 DOI: 10.1073/Pnas.1815356116  0.529
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  0.336
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  0.37
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  0.418
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  0.448
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  0.598
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  0.643
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  0.631
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  0.72
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  0.587
2018 Petyuk VA, Chang R, Ramirez-Restrepo M, Beckmann ND, Henrion MYR, Piehowski PD, Zhu K, Wang S, Clarke J, Huentelman MJ, Xie F, Andreev V, Engel A, Guettoche T, Navarro L, ... ... Smith RD, et al. The human brainome: network analysis identifies HSPA2 as a novel Alzheimer's disease target. Brain : a Journal of Neurology. PMID 30137212 DOI: 10.1093/Brain/Awy215  0.625
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  0.657
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  0.62
2018 Piehowski PD, Petyuk VA, Sontag RL, Gritsenko MA, Weitz KK, Fillmore TL, Moon J, Makhlouf H, Chuaqui RF, Boja ES, Rodriguez H, Lee JSH, Smith RD, Carrick DM, Liu T, et al. Residual tissue repositories as a resource for population-based cancer proteomic studies. Clinical Proteomics. 15: 26. PMID 30087585 DOI: 10.1186/S12014-018-9202-4  0.653
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  0.663
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  0.409
2018 Guo J, Wilken S, Jimenez V, Choi CJ, Ansong C, Dannebaum R, Sudek L, Milner DS, Bachy C, Reistetter EN, Elrod VA, Klimov D, Purvine SO, Wei CL, Kunde-Ramamoorthy G, ... ... Smith RD, et al. Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation. Nature Microbiology. 3: 781-790. PMID 29946165 DOI: 10.1038/S41564-018-0178-7  0.302
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  0.655
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  0.747
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  0.599
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  0.603
2018 Zhu Y, Clair G, Chrisler W, Shen Y, Zhao R, Shukla A, Moore R, Misra R, Pryhuber G, Smith R, Ansong C, Kelly RT. Proteomic analysis of single mammalian cells enabled by microfluidic nanodroplet sample preparation and ultrasensitive nanoLC-MS. Angewandte Chemie (International Ed. in English). PMID 29797682 DOI: 10.1002/Anie.201802843  0.336
2018 Rodland KD, Piehowski P, Smith RD. Moonshot Objectives: Catalyze New Scientific Breakthroughs-Proteogenomics. Cancer Journal (Sudbury, Mass.). 24: 117-121. PMID 29794536 DOI: 10.1097/Ppo.0000000000000315  0.618
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  0.67
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  0.741
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  0.347
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  0.72
2018 Liu T, Rodland KD, Smith RD. Characterization of the Ovarian Tumor Peptidome. Vitamins and Hormones. 107: 515-531. PMID 29544642 DOI: 10.1016/Bs.Vh.2018.01.020  0.305
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  0.665
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  0.684
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  0.715
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  0.525
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  0.617
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  0.331
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  0.617
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  0.676
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  0.636
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  0.65
2017 Zhou JY, Chen L, Zhang B, Tian Y, Liu T, Thomas SN, Chen L, Schnaubelt M, Boja E, Hiltke T, Kinsinger CR, Rodriguez H, Davies SR, Li S, Snider JE, ... ... Smith RD, et al. Quality Assessments of Long-term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues. Journal of Proteome Research. PMID 29124938 DOI: 10.1021/Acs.Jproteome.7B00362  0.387
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  0.39
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  0.66
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  0.698
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  0.699
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  0.682
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  0.367
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  0.386
2017 Dhondt I, Petyuk VA, Bauer S, Brewer HM, Smith RD, Depuydt G, Braeckman BP. Changes of protein turnover in aging Caenorhabditis elegans. Molecular & Cellular Proteomics : McP. PMID 28679685 DOI: 10.1074/Mcp.Ra117.000049  0.313
2017 Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T. Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease. The Journal of Pathology. PMID 28657654 DOI: 10.1002/Path.4929  0.307
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  0.573
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  0.647
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  0.324
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  0.723
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  0.624
2017 Gao H, Makarov A, Smith RD. 2016 ASMS Workshop Review: Next Generation LC/MS: Critical Insights and Future Perspectives. Journal of the American Society For Mass Spectrometry. PMID 28417304 DOI: 10.1007/S13361-017-1664-5  0.331
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  0.671
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  0.715
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  0.678
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  0.571
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  0.63
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  0.357
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  0.6
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  0.652
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  0.669
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  0.699
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  0.754
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  0.785
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  0.671
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  0.682
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  0.662
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  0.435
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  0.708
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  0.659
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  0.663
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  0.631
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  0.528
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  0.663
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  0.323
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  0.606
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  0.67
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  0.647
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  0.643
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  0.313
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  0.314
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  0.344
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  0.641
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  0.577
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  0.493
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  0.349
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  0.436
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  0.374
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  0.642
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  0.502
2016 Chen TC, Ibrahim YM, Webb IK, Garimella SV, Zhang X, Hamid AM, Deng L, Karnesky WE, Prost SA, Sandoval JA, Norheim RV, Anderson GA, Tolmachev AV, Baker ES, Smith RD. Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations. Analytical Chemistry. PMID 26752262 DOI: 10.1021/Acs.Analchem.5B03910  0.616
2016 Huang EL, Piehowski PD, Orton DJ, Moore RJ, Qian WJ, Casey CP, Sun X, Dey SK, Burnum-Johnson KE, Smith RD. SNaPP: Simplified Nano-Proteomics Platform for reproducible global proteomic analysis of nanogram protein quantities. Endocrinology. en20151821. PMID 26745641 DOI: 10.1210/En.2015-1821  0.674
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  0.741
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  0.377
2016 Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, Brümmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ. Author response: Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes Elife. DOI: 10.7554/Elife.15614.024  0.574
2016 Myers A, Chang R, Petyuk VA, Ramirez-Restrepo M, Beckmann ND, Henrion MY, Zhu K, Wang S, Piehowski PD, Clarke J, Huentelman MJ, Xie F, Andreev V, Engel A, Guettoche T, ... ... Smith R, et al. O2-06-01: The Human Brainome: Human Brain Genome, Transcriptome, and Proteome Integration Alzheimer's & Dementia. 12: P237-P238. DOI: 10.1016/J.Jalz.2016.06.424  0.586
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  0.389
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  0.368
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  0.395
2015 Annesley T, Diamandis E, Bachmann L, Hanash S, Hart B, Javahery R, Singh R, Smith R. A Spectrum of Views on Clinical Mass Spectrometry. Clinical Chemistry. PMID 26553793 DOI: 10.1373/Clinchem.2015.250258  0.341
2015 Hamid AM, Ibrahim YM, Garimella SV, Webb IK, Deng L, Chen TC, Anderson GA, Prost SA, Norheim RV, Tolmachev AV, Smith RD. Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations. Analytical Chemistry. PMID 26510005 DOI: 10.1021/Acs.Analchem.5B02481  0.362
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  0.544
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  0.599
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  0.351
2015 Garimella SV, Ibrahim YM, Webb IK, Ipsen AB, Chen TC, Tolmachev AV, Baker ES, Anderson GA, Smith RD. Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch. The Analyst. 140: 6845-52. PMID 26289106 DOI: 10.1039/C5An00844A  0.6
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  0.382
2015 Ibrahim YM, Baker ES, Danielson WF, Norheim RV, Prior DC, Anderson GA, Belov ME, Smith RD. Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer. International Journal of Mass Spectrometry. 377: 655-662. PMID 26185483 DOI: 10.1016/J.Ijms.2014.07.034  0.669
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  0.326
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  0.306
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  0.689
2015 Chen TC, Fillmore TL, Prost SA, Moore RJ, Ibrahim YM, Smith RD. An Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadruple Mass Spectrometry. Analytical Chemistry. PMID 26107611 DOI: 10.1021/Acs.Analchem.5B01482  0.412
2015 Baker ES, Burnum-Johnson KE, Ibrahim YM, Orton DJ, Monroe ME, Kelly RT, Moore RJ, Zhang X, Théberge R, Costello CE, Smith RD. Enhancing bottom-up and top-down proteomic measurements with ion mobility separations. Proteomics. PMID 26046661 DOI: 10.1002/Pmic.201500048  0.676
2015 Wu C, Monroe ME, Xu Z, Slysz GW, Payne SH, Rodland KD, Liu T, Smith RD. An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics. Journal of the American Society For Mass Spectrometry. PMID 26015166 DOI: 10.1007/S13361-015-1169-Z  0.407
2015 Zhang X, Garimella SV, Prost SA, Webb IK, Chen TC, Tang K, Tolmachev AV, Norheim RV, Baker ES, Anderson GA, Ibrahim YM, Smith RD. Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations. Analytical Chemistry. 87: 6010-6. PMID 25971536 DOI: 10.1021/Acs.Analchem.5B00214  0.598
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  0.564
2015 He J, Schepmoes AA, Shi T, Wu C, Fillmore TL, Gao Y, Smith RD, Qian WJ, Rodland KD, Liu T, Camp DG, Rastogi A, Tan SH, Yan W, Mohamed AA, et al. Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods. Journal of Translational Medicine. 13: 54. PMID 25889691 DOI: 10.1186/S12967-015-0418-Z  0.301
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  0.618
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  0.403
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  0.357
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  0.431
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  0.568
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  0.515
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  0.611
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  0.301
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  0.331
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  0.337
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  0.378
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  0.376
2014 Hyung SW, Piehowski PD, Moore RJ, Orton DJ, Schepmoes AA, Clauss TR, Chu RK, Fillmore TL, Brewer H, Liu T, Zhao R, Smith RD. Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid. Analytical and Bioanalytical Chemistry. 406: 7117-25. PMID 25192788 DOI: 10.1007/S00216-014-8058-3  0.675
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  0.359
2014 Wu C, Shi T, Brown JN, He J, Gao Y, Fillmore TL, Shukla AK, Moore RJ, Camp DG, Rodland KD, Qian WJ, Liu T, Smith RD. Expediting SRM assay development for large-scale targeted proteomics experiments. Journal of Proteome Research. 13: 4479-87. PMID 25145539 DOI: 10.1021/Pr500500D  0.325
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  0.358
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  0.57
2014 Kronewitter SR, Marginean I, Cox JT, Zhao R, Hagler CD, Shukla AK, Carlson TS, Adkins JN, Camp DG, Moore RJ, Rodland KD, Smith RD. Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry. Analytical Chemistry. 86: 8700-10. PMID 25118826 DOI: 10.1021/Ac501839B  0.338
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  0.643
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  0.395
2014 Kronewitter SR, Slysz GW, Marginean I, Hagler CD, LaMarche BL, Zhao R, Harris MY, Monroe ME, Polyukh CA, Crowell KL, Fillmore TL, Carlson TS, Camp DG, Moore RJ, Payne SH, ... ... Smith RD, et al. GlyQ-IQ: glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization. Analytical Chemistry. 86: 6268-76. PMID 24881670 DOI: 10.1021/Ac501492F  0.424
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  0.532
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  0.751
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  0.621
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  0.348
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  0.343
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  0.342
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  0.404
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  0.308
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  0.323
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  0.414
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  0.328
2014 Baker ES, Burnum-Johnson KE, Jacobs JM, Diamond DL, Brown RN, Ibrahim YM, Orton DJ, Piehowski PD, Purdy DE, Moore RJ, Danielson WF, Monroe ME, Crowell KL, Slysz GW, Gritsenko MA, ... ... Smith RD, et al. Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry. Molecular & Cellular Proteomics : McP. 13: 1119-27. PMID 24403597 DOI: 10.1074/Mcp.M113.034595  0.789
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  0.361
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  0.378
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  0.43
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  0.539
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  0.366
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  0.379
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  0.314
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  0.348
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  0.665
2014 Shi T, He J, Wu C, Fillmore TL, Schepmoes AA, Rubin M, Siddiqui J, Wei J, Chinnaiyan A, Liu A, Smith RD, Kagan J, Srivastava S, Rodland KD, Qian W, et al. Abstract 2483: An antibody-independent, complementary SRM strategy for ultrasensitive and multiplexed quantification of cancer biomarker candidates Cancer Research. 74: 2483-2483. DOI: 10.1158/1538-7445.Am2014-2483  0.366
2014 Myers A, Ramirez-Restrepo M, Petyuk V, Piehowski P, Gaiteri C, Xie F, Smith R. P1-047: THE HUMAN BRAINOME: GENOME, TRANSCRIPTOME, AND PROTEOME INTERACTION IN HUMAN CORTEX Alzheimer's & Dementia. 10: P320-P320. DOI: 10.1016/J.Jalz.2014.05.282  0.586
2014 Shvartsburg AA, Ibrahim YM, Smith RD. Erratum to: Differential Ion Mobility Separations in up to 100% Helium Using Microchips Journal of the American Society For Mass Spectrometry. 25: 1995-1995. DOI: 10.1007/S13361-014-0984-Y  0.336
2013 Crowell KL, Baker ES, Payne SH, Ibrahim YM, Monroe ME, Slysz GW, LaMarche BL, Petyuk VA, Piehowski PD, Danielson WF, Anderson GA, Smith RD. Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry. International Journal of Mass Spectrometry. 354: 312-317. PMID 25089116 DOI: 10.1016/J.Ijms.2013.06.028  0.789
2013 Smith RD, Loa JA, Barinaga CJ, Edmonds CG, Udseth HR. Collisional activation and collision-activated dissociation of large multiply charged polypeptides and proteins produced by electrospray ionization. Journal of the American Society For Mass Spectrometry. 1: 53-65. PMID 24248611 DOI: 10.1016/1044-0305(90)80006-9  0.365
2013 Winger BE, Hofstadler SA, Bruce JE, Udseth HR, Smith RD. High-resolution accurate mass measurements of biomolecules using a new electrospray ionization ion cyclotron resonance mass spectrometer. Journal of the American Society For Mass Spectrometry. 4: 566-77. PMID 24227643 DOI: 10.1016/1044-0305(93)85018-S  0.388
2013 Loo JA, Hu P, Smith RD. Interaction of angiotensin peptides and zinc metal ions probed by electrospray ionization mass spectrometry. Journal of the American Society For Mass Spectrometry. 5: 959-65. PMID 24226385 DOI: 10.1016/1044-0305(94)80014-6  0.373
2013 Hofstadler SA, Wahl JH, Bakhtiar R, Anderson GA, Bruce JE, Smith RD. Capillary electrophoresis fourier transform ion cyclotron resonance mass spectrometry with sustained off-resonance irradiation for the characterization of protein and peptide mixtures. Journal of the American Society For Mass Spectrometry. 5: 894-9. PMID 24226235 DOI: 10.1016/1044-0305(94)87014-4  0.409
2013 Goodlelt DR, Ogorzalek Loo RR, Loo JA, Wahl JH, Udseth HR, Smith RD. A study of the thermal denaturation of ribonuclease S by electrospray ionization mass spectrometry. Journal of the American Society For Mass Spectrometry. 5: 614-22. PMID 24221963 DOI: 10.1016/1044-0305(94)85002-X  0.391
2013 Anderson LN, Culley DE, Hofstad BA, Chauvigné-Hines LM, Zink EM, Purvine SO, Smith RD, Callister SJ, Magnuson JM, Wright AT. Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30. Molecular Biosystems. 9: 2992-3000. PMID 24121482 DOI: 10.1039/C3Mb70333A  0.305
2013 Schutzer SE, Angel TE, Liu T, Schepmoes AA, Xie F, Bergquist J, Vécsei L, Zadori D, Camp DG, Holland BK, Smith RD, Coyle PK. Gray matter is targeted in first-attack multiple sclerosis. Plos One. 8: e66117. PMID 24039694 DOI: 10.1371/Journal.Pone.0066117  0.354
2013 Crowell KL, Slysz GW, Baker ES, LaMarche BL, Monroe ME, Ibrahim YM, Payne SH, Anderson GA, Smith RD. LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. Bioinformatics (Oxford, England). 29: 2804-5. PMID 24008421 DOI: 10.1093/Bioinformatics/Btt465  0.647
2013 Shi T, Fillmore TL, Gao Y, Zhao R, He J, Schepmoes AA, Nicora CD, Wu C, Chambers JL, Moore RJ, Kagan J, Srivastava S, Liu AY, Rodland KD, Liu T, ... ... Smith RD, et al. Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis. Analytical Chemistry. 85: 9196-203. PMID 24004026 DOI: 10.1021/Ac402105S  0.387
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  0.536
2013 Sun X, Tang K, Smith RD, Kelly RT. Controlled dispensing and mixing of pico- to nanoliter volumes using on-demand droplet-based microfluidics. Microfluidics and Nanofluidics. 15: 117-126. PMID 23935562 DOI: 10.1007/S10404-012-1133-1  0.318
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  0.531
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  0.534
2013 Shvartsburg AA, Smith RD. Separation of protein conformers by differential ion mobility in hydrogen-rich gases. Analytical Chemistry. 85: 6967-73. PMID 23855890 DOI: 10.1021/Ac4015963  0.382
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  0.644
2013 Wang C, Lee CS, Smith RD, Tang K. Capillary isotachophoresis-nanoelectrospray ionization-selected reaction monitoring MS via a novel sheathless interface for high sensitivity sample quantification. Analytical Chemistry. 85: 7308-15. PMID 23789856 DOI: 10.1021/Ac401202C  0.411
2013 Kim JS, Dai Z, Aryal UK, Moore RJ, Camp DG, Baker SE, Smith RD, Qian WJ. Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing. Analytical Chemistry. 85: 6826-32. PMID 23772796 DOI: 10.1021/Ac401000Q  0.38
2013 Shi T, Sun X, Gao Y, Fillmore TL, Schepmoes AA, Zhao R, He J, Moore RJ, Kagan J, Rodland KD, Liu T, Liu AY, Smith RD, Tang K, Camp DG, et al. Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion. Journal of Proteome Research. 12: 3353-61. PMID 23763644 DOI: 10.1021/Pr400178V  0.33
2013 Ansong C, Wu S, Meng D, Liu X, Brewer HM, Deatherage Kaiser BL, Nakayasu ES, Cort JR, Pevzner P, Smith RD, Heffron F, Adkins JN, Pasa-Tolic L. Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions. Proceedings of the National Academy of Sciences of the United States of America. 110: 10153-8. PMID 23720318 DOI: 10.1073/Pnas.1221210110  0.35
2013 Zhou JY, Krovvidi RK, Gao Y, Gao H, Petritis BO, De AK, Miller-Graziano CL, Bankey PE, Petyuk VA, Nicora CD, Clauss TR, Moore RJ, Shi T, Brown JN, Kaushal A, ... ... Smith RD, et al. Trauma-associated human neutrophil alterations revealed by comparative proteomics profiling. Proteomics. Clinical Applications. 7: 571-83. PMID 23589343 DOI: 10.1002/Prca.201200109  0.344
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  0.592
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  0.655
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  0.686
2013 Merkley ED, Baker ES, Crowell KL, Orton DJ, Taverner T, Ansong C, Ibrahim YM, Burnet MC, Cort JR, Anderson GA, Smith RD, Adkins JN. Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking. Journal of the American Society For Mass Spectrometry. 24: 444-9. PMID 23423792 DOI: 10.1007/S13361-012-0565-X  0.628
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  0.629
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  0.544
2013 Shvartsburg AA, Seim TA, Danielson WF, Norheim R, Moore RJ, Anderson GA, Smith RD. High-definition differential ion mobility spectrometry with resolving power up to 500. Journal of the American Society For Mass Spectrometry. 24: 109-14. PMID 23345059 DOI: 10.1007/S13361-012-0517-5  0.347
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  0.651
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  0.576
2013 Su D, Shukla AK, Chen B, Kim JS, Nakayasu E, Qu Y, Aryal U, Weitz K, Clauss TR, Monroe ME, Camp DG, Bigelow DJ, Smith RD, Kulkarni RN, Qian WJ. Quantitative site-specific reactivity profiling of S-nitrosylation in mouse skeletal muscle using cysteinyl peptide enrichment coupled with mass spectrometry. Free Radical Biology & Medicine. 57: 68-78. PMID 23277143 DOI: 10.1016/J.Freeradbiomed.2012.12.010  0.34
2013 Kim JS, Monroe ME, Camp DG, Smith RD, Qian WJ. In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics. Journal of Proteome Research. 12: 910-6. PMID 23268687 DOI: 10.1021/Pr300955F  0.363
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  0.668
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  0.642
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  0.623
2013 He J, Sun X, Shi T, Schepmoes A, Fillmore T, Petyuk V, Xie F, Gritsenko M, Yang F, Kitabayashi N, Chae SS, Rubin M, Siddiqui J, Wei J, Chinnaiyan A, ... ... Smith R, et al. Abstract 3207: Application of an antibody-free, highly sensitive PRISM-SRM proteomics approach for monitoring low abundance proteins and protein isoforms in cell lines and tumor tissue. Cancer Research. 73: 3207-3207. DOI: 10.1158/1538-7445.Am2013-3207  0.327
2012 Shvartsburg AA, Smith RD. High-resolution differential ion mobility spectrometry of a protein. Analytical Chemistry. 85: 10-3. PMID 23244633 DOI: 10.1021/Ac3029129  0.381
2012 Karpievitch YV, Dabney AR, Smith RD. Normalization and missing value imputation for label-free LC-MS analysis. Bmc Bioinformatics. 13: S5. PMID 23176322 DOI: 10.1186/1471-2105-13-S16-S5  0.317
2012 Chauvigné-Hines LM, Anderson LN, Weaver HM, Brown JN, Koech PK, Nicora CD, Hofstad BA, Smith RD, Wilkins MJ, Callister SJ, Wright AT. Suite of activity-based probes for cellulose-degrading enzymes. Journal of the American Chemical Society. 134: 20521-32. PMID 23176123 DOI: 10.1021/Ja309790W  0.363
2012 Wang C, Lee CS, Smith RD, Tang K. Ultrasensitive sample quantitation via selected reaction monitoring using CITP/CZE-ESI-triple quadrupole MS. Analytical Chemistry. 84: 10395-403. PMID 23140208 DOI: 10.1021/Ac302616M  0.406
2012 Merkley ED, Anderson BJ, Park J, Belchik SM, Shi L, Monroe ME, Smith RD, Lipton MS. Detection and identification of heme c-modified peptides by histidine affinity chromatography, high-performance liquid chromatography-mass spectrometry, and database searching. Journal of Proteome Research. 11: 6147-58. PMID 23082897 DOI: 10.1021/Pr3007914  0.387
2012 Maxwell E, Tan Y, Tan Y, Hu H, Benson G, Aizikov K, Conley S, Staples GO, Slysz GW, Smith RD, Zaia J. GlycReSoft: a software package for automated recognition of glycans from LC/MS data. Plos One. 7: e45474. PMID 23049804 DOI: 10.1371/Journal.Pone.0045474  0.373
2012 Tian Z, Tolić N, Zhao R, Moore RJ, Hengel SM, Robinson EW, Stenoien DL, Wu S, Smith RD, Paša-Tolić L. Enhanced top-down characterization of histone post-translational modifications. Genome Biology. 13: R86. PMID 23034525 DOI: 10.1186/Gb-2012-13-10-R86  0.755
2012 Marginean I, Kronewitter SR, Moore RJ, Slysz GW, Monroe ME, Anderson G, Tang K, Smith RD. Improving N-glycan coverage using HPLC-MS with electrospray ionization at subambient pressure. Analytical Chemistry. 84: 9208-13. PMID 23025344 DOI: 10.1021/Ac301961U  0.397
2012 Shi T, Fillmore TL, Sun X, Zhao R, Schepmoes AA, Hossain M, Xie F, Wu S, Kim JS, Jones N, Moore RJ, Pasa-Tolić L, Kagan J, Rodland KD, Liu T, ... ... Smith RD, et al. Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum. Proceedings of the National Academy of Sciences of the United States of America. 109: 15395-400. PMID 22949669 DOI: 10.1073/Pnas.1204366109  0.345
2012 Baker ES, Liu T, Petyuk VA, Burnum-Johnson KE, Ibrahim YM, Anderson GA, Smith RD. Mass spectrometry for translational proteomics: progress and clinical implications. Genome Medicine. 4: 63. PMID 22943415 DOI: 10.1186/Gm364  0.633
2012 Angel TE, Jacobs JM, Smith RP, Pasternack MS, Elias S, Gritsenko MA, Shukla A, Gilmore EC, McCarthy C, Camp DG, Smith RD, Warren HS. Cerebrospinal fluid proteome of patients with acute Lyme disease. Journal of Proteome Research. 11: 4814-22. PMID 22900834 DOI: 10.1021/Pr300577P  0.302
2012 Brown RN, Sanford JA, Park JH, Deatherage BL, Champion BL, Smith RD, Heffron F, Adkins JN. A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions. International Journal of Proteomics. 2012: 123076. PMID 22900174 DOI: 10.1155/2012/123076  0.312
2012 Shvartsburg AA, Smith RD. Protein analyses using differential ion mobility microchips with mass spectrometry. Analytical Chemistry. 84: 7297-300. PMID 22889348 DOI: 10.1021/Ac3018636  0.459
2012 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  0.55
2012 Liu T, Hossain M, Schepmoes AA, Fillmore TL, Sokoll LJ, Kronewitter SR, Izmirlian G, Shi T, Qian WJ, Leach RJ, Thompson IM, Chan DW, Smith RD, Kagan J, Srivastava S, et al. Analysis of serum total and free PSA using immunoaffinity depletion coupled to SRM: correlation with clinical immunoassay tests. Journal of Proteomics. 75: 4747-57. PMID 22846433 DOI: 10.1016/J.Jprot.2012.01.035  0.363
2012 Xie F, Smith RD, Shen Y. Advanced proteomic liquid chromatography. Journal of Chromatography. A. 1261: 78-90. PMID 22840822 DOI: 10.1016/J.Chroma.2012.06.098  0.386
2012 Shvartsburg AA, Zheng Y, Smith RD, Kelleher NL. Separation of variant methylated histone tails by differential ion mobility. Analytical Chemistry. 84: 6317-20. PMID 22812477 DOI: 10.1021/Ac301541R  0.376
2012 Burnum KE, Hirota Y, Baker ES, Yoshie M, Ibrahim YM, Monroe ME, Anderson GA, Smith RD, Daikoku T, Dey SK. Uterine deletion of Trp53 compromises antioxidant responses in the mouse decidua. Endocrinology. 153: 4568-79. PMID 22759378 DOI: 10.1210/En.2012-1335  0.533
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  0.645
2012 Lee JH, Hyung SW, Mun DG, Jung HJ, Kim H, Lee H, Kim SJ, Park KS, Moore RJ, Smith RD, Lee SW. Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses. Journal of Proteome Research. 11: 4373-81. PMID 22709424 DOI: 10.1021/Pr3004166  0.313
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  0.562
2012 Shi T, Su D, Liu T, Tang K, Camp DG, Qian WJ, Smith RD. Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics. Proteomics. 12: 1074-92. PMID 22577010 DOI: 10.1002/Pmic.201100436  0.349
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  0.517
2012 Shvartsburg AA, Zheng Y, Smith RD, Kelleher NL. Ion mobility separation of variant histone tails extending to the "middle-down" range. Analytical Chemistry. 84: 4271-6. PMID 22559289 DOI: 10.1021/Ac300612Y  0.384
2012 Andreev VP, Petyuk VA, Brewer HM, Karpievitch YV, Xie F, Clarke J, Camp D, Smith RD, Lieberman AP, Albin RL, Nawaz Z, El Hokayem J, Myers AJ. Label-free quantitative LC-MS proteomics of Alzheimer's disease and normally aged human brains. Journal of Proteome Research. 11: 3053-67. PMID 22559202 DOI: 10.1021/Pr3001546  0.356
2012 Wang X, Anderson GA, Smith RD, Dabney AR. A hybrid approach to protein differential expression in mass spectrometry-based proteomics. Bioinformatics (Oxford, England). 28: 1586-91. PMID 22522136 DOI: 10.1093/Bioinformatics/Bts193  0.357
2012 Angel TE, Aryal UK, Hengel SM, Baker ES, Kelly RT, Robinson EW, Smith RD. Mass spectrometry-based proteomics: existing capabilities and future directions. Chemical Society Reviews. 41: 3912-28. PMID 22498958 DOI: 10.1039/C2Cs15331A  0.828
2012 Waters KM, Liu T, Quesenberry RD, Willse AR, Bandyopadhyay S, Kathmann LE, Weber TJ, Smith RD, Wiley HS, Thrall BD. Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data. Plos One. 7: e34515. PMID 22479638 DOI: 10.1371/Journal.Pone.0034515  0.303
2012 Yang F, Shen Y, Camp DG, Smith RD. High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Review of Proteomics. 9: 129-34. PMID 22462785 DOI: 10.1586/Epr.12.15  0.354
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  0.605
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  0.599
2012 Zhou JY, Dann GP, Shi T, Wang L, Gao X, Su D, Nicora CD, Shukla AK, Moore RJ, Liu T, Camp DG, Smith RD, Qian WJ. Simple sodium dodecyl sulfate-assisted sample preparation method for LC-MS-based proteomics applications. Analytical Chemistry. 84: 2862-7. PMID 22339560 DOI: 10.1021/Ac203394R  0.411
2012 Cao L, Bryant DA, Schepmoes AA, Vogl K, Smith RD, Lipton MS, Callister SJ. Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically. Photosynthesis Research. 110: 153-68. PMID 22249883 DOI: 10.1007/S11120-011-9711-8  0.323
2012 Smith RD. Mass spectrometry in biomarker applications: From untargeted discovery to targeted verification, and implications for platform convergence and clinical application Clinical Chemistry. 58: 528-530. PMID 22194635 DOI: 10.1373/Clinchem.2011.180596  0.408
2012 Wang L, Aryal UK, Dai Z, Mason AC, Monroe ME, Tian ZX, Zhou JY, Su D, Weitz KK, Liu T, Camp DG, Smith RD, Baker SE, Qian WJ. Mapping N-linked glycosylation sites in the secretome and whole cells of Aspergillus niger using hydrazide chemistry and mass spectrometry. Journal of Proteome Research. 11: 143-56. PMID 22136231 DOI: 10.1021/Pr200916K  0.3
2012 Aryal UK, Stöckel J, Welsh EA, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB, Jacobs JM. Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light. Journal of Proteome Research. 11: 609-19. PMID 22060561 DOI: 10.1021/Pr200959X  0.34
2012 Shen Y, Tolić N, Purvine SO, Smith RD. Improving collision induced dissociation (CID), high energy collision dissociation (HCD), and electron transfer dissociation (ETD) fourier transform MS/MS degradome-peptidome identifications using high accuracy mass information. Journal of Proteome Research. 11: 668-77. PMID 22054047 DOI: 10.1021/Pr200597J  0.42
2012 Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA. Protein identification using top-down. Molecular & Cellular Proteomics : McP. 11: M111.008524. PMID 22027200 DOI: 10.1074/Mcp.M111.008524  0.603
2012 Shi T, Zhou JY, Gritsenko MA, Hossain M, Camp DG, Smith RD, Qian WJ. IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomics biomarker discovery. Methods (San Diego, Calif.). 56: 246-53. PMID 21925605 DOI: 10.1016/J.Ymeth.2011.09.001  0.379
2012 Bruce JE, Anderson GA, Udseth HR, Smith RD. Large Molecule Characterization Based upon Individual Ion Detection with Electrospray Ionization-FTICR Mass Spectrometry. Analytical Chemistry. 70: 519-25. PMID 21644751 DOI: 10.1021/Ac9711706  0.362
2012 Liu T, Shi T, Hossain M, Schepmoes A, Fillmore T, Sokoll LJ, Chan D, Leach R, Thompson I, Smith RD, Kagan J, Srivastava S, Rodland KD, Camp DG, Qian W. Abstract 1268: Accurate measurement of serum total and free PSA using immunoaffinity depletion coupled to SRM: Correlation with clinical immunoassays Cancer Research. 72: 1268-1268. DOI: 10.1158/1538-7445.Am2012-1268  0.345
2012 Schnaar R, Paulson JC, Macauley MS, Nycholat C, Pfrengle F, Rademacher C, Mahan A, Dionne K, Suscovich T, Alter G, Katoh T, Kiwamoto T, Brummet M, Bochner B, Tiemeyer M, ... ... Smith R, et al. Program and abstracts for the 2012 Joint Meeting of the Society for Glycobiology & American Society for Matrix Biology Glycobiology. 22: 1518-1650. DOI: 10.1093/Glycob/Cws127  0.436
2012 Tolmachev AV, Robinson EW, Smith RD, Leach FE, Futrell JH, Paa-Tolić L. A conceptual approach for FT-ICR cell harmonization utilizing external shim electrodes International Journal of Mass Spectrometry. 325: 45-50. DOI: 10.1016/J.Ijms.2012.06.027  0.582
2011 Aryal UK, Stöckel J, Krovvidi RK, Gritsenko MA, Monroe ME, Moore RJ, Koppenaal DW, Smith RD, Pakrasi HB, Jacobs JM. Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles. Bmc Systems Biology. 5: 194. PMID 22133144 DOI: 10.1186/1752-0509-5-194  0.311
2011 Shvartsburg AA, Smith RD. Accelerated high-resolution differential ion mobility separations using hydrogen. Analytical Chemistry. 83: 9159-66. PMID 22074292 DOI: 10.1021/Ac202386W  0.357
2011 Kim JS, Fillmore TL, Liu T, Robinson E, Hossain M, Champion BL, Moore RJ, Camp DG, Smith RD, Qian WJ. 18O-labeled proteome reference as global internal standards for targeted quantification by selected reaction monitoring-mass spectrometry. Molecular & Cellular Proteomics : McP. 10: M110.007302. PMID 21988777 DOI: 10.1074/Mcp.M110.007302  0.356
2011 Zhang H, Burnum KE, Luna ML, Petritis BO, Kim JS, Qian WJ, Moore RJ, Heredia-Langner A, Webb-Robertson BJ, Thrall BD, Camp DG, Smith RD, Pounds JG, Liu T. Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size. Proteomics. 11: 4569-77. PMID 21956884 DOI: 10.1002/Pmic.201100037  0.332
2011 Tang K, Page JS, Marginean I, Kelly RT, Smith RD. Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface. Journal of the American Society For Mass Spectrometry. 22: 1318-25. PMID 21953185 DOI: 10.1007/S13361-011-0135-7  0.367
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  0.622
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  0.518
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  0.682
2011 Shvartsburg AA, Creese AJ, Smith RD, Cooper HJ. Separation of a set of peptide sequence isomers using differential ion mobility spectrometry. Analytical Chemistry. 83: 6918-23. PMID 21863819 DOI: 10.1021/Ac201640D  0.376
2011 Zhang H, Yang F, Qian WJ, Brown RN, Wang Y, Merkley ED, Merkley EE, Park JH, Monroe ME, Purvine SO, Moore RJ, Shi L, Fredrickson JK, PaÅ¡a-Tolić L, Smith RD, et al. Identification of c-type heme-containing peptides using nonactivated immobilized metal affinity chromatography resin enrichment and higher-energy collisional dissociation. Analytical Chemistry. 83: 7260-8. PMID 21740036 DOI: 10.1021/Ac2000829  0.341
2011 Ghazalpour A, Bennett B, Petyuk VA, Orozco L, Hagopian R, Mungrue IN, Farber CR, Sinsheimer J, Kang HM, Furlotte N, Park CC, Wen PZ, Brewer H, Weitz K, Camp DG, ... ... Smith RD, et al. Comparative analysis of proteome and transcriptome variation in mouse. Plos Genetics. 7: e1001393. PMID 21695224 DOI: 10.1371/Journal.Pgen.1001393  0.307
2011 Stanley JR, Adkins JN, Slysz GW, Monroe ME, Purvine SO, Karpievitch YV, Anderson GA, Smith RD, Dabney AR. A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics. Analytical Chemistry. 83: 6135-40. PMID 21692516 DOI: 10.1021/Ac2009806  0.343
2011 Ibrahim YM, Shvartsburg AA, Smith RD, Belov ME. Ultrasensitive identification of localization variants of modified peptides using ion mobility spectrometry. Analytical Chemistry. 83: 5617-23. PMID 21692493 DOI: 10.1021/Ac200719N  0.447
2011 Shen Y, Tolić N, Xie F, Zhao R, Purvine SO, Schepmoes AA, Moore RJ, Anderson GA, Smith RD. Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods. Journal of Proteome Research. 10: 3929-43. PMID 21678914 DOI: 10.1021/Pr200052C  0.386
2011 Shvartsburg AA, Singer D, Smith RD, Hoffmann R. Ion mobility separation of isomeric phosphopeptides from a protein with variant modification of adjacent residues. Analytical Chemistry. 83: 5078-85. PMID 21667994 DOI: 10.1021/Ac200985S  0.455
2011 Sun X, Kelly RT, Tang K, Smith RD. Membrane-based emitter for coupling microfluidics with ultrasensitive nanoelectrospray ionization-mass spectrometry. Analytical Chemistry. 83: 5797-803. PMID 21657269 DOI: 10.1021/Ac200960H  0.331
2011 Xie F, Liu T, Qian WJ, Petyuk VA, Smith RD. Liquid chromatography-mass spectrometry-based quantitative proteomics. The Journal of Biological Chemistry. 286: 25443-9. PMID 21632532 DOI: 10.1074/Jbc.R110.199703  0.411
2011 Zhang Q, Monroe ME, Schepmoes AA, Clauss TR, Gritsenko MA, Meng D, Petyuk VA, Smith RD, Metz TO. Comprehensive identification of glycated peptides and their glycation motifs in plasma and erythrocytes of control and diabetic subjects. Journal of Proteome Research. 10: 3076-88. PMID 21612289 DOI: 10.1021/Pr200040J  0.568
2011 Qian WJ, Petritis BO, Nicora CD, Smith RD. Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics. Methods of Molecular Biology. 753: 43-54. PMID 21604114 DOI: 10.1007/978-1-61779-148-2_3  0.317
2011 Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner PA. Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nature Methods. 8: 587-91. PMID 21572408 DOI: 10.1038/Nmeth.1609  0.357
2011 Shukla A, Zhang R, Orton DJ, Zhao R, Clauss TR, Moore R, Smith RD. Formation of iron complexes from trifluoroacetic acid based liquid chromatography mobile phases as interference ions in liquid chromatography/electrospray ionization mass spectrometric analysis. Rapid Communications in Mass Spectrometry : Rcm. 25: 1452-6. PMID 21504012 DOI: 10.1002/Rcm.5017  0.406
2011 Wang Y, Yang F, Gritsenko MA, Wang Y, Clauss T, Liu T, Shen Y, Monroe ME, Lopez-Ferrer D, Reno T, Moore RJ, Klemke RL, Camp DG, Smith RD. Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics. 11: 2019-26. PMID 21500348 DOI: 10.1002/Pmic.201000722  0.338
2011 Schoenherr RM, Kelly-Spratt KS, Lin C, Whiteaker JR, Liu T, Holzman T, Coleman I, Feng LC, Lorentzen TD, Krasnoselsky AL, Wang P, Liu Y, Gurley KE, Amon LM, Schepmoes AA, ... ... Smith RD, et al. Proteome and transcriptome profiles of a Her2/Neu-driven mouse model of breast cancer. Proteomics. Clinical Applications. 5: 179-88. PMID 21448875 DOI: 10.1002/Prca.201000037  0.353
2011 Schutzer SE, Angel TE, Liu T, Schepmoes AA, Clauss TR, Adkins JN, Camp DG, Holland BK, Bergquist J, Coyle PK, Smith RD, Fallon BA, Natelson BH. Distinct cerebrospinal fluid proteomes differentiate post-treatment lyme disease from chronic fatigue syndrome. Plos One. 6: e17287. PMID 21383843 DOI: 10.1371/Journal.Pone.0017287  0.347
2011 Gonzalez RM, Zhang Q, Zangar RC, Smith RD, Metz TO. Development of a fibrinogen-specific sandwich enzyme-linked immunosorbent assay microarray assay for distinguishing between blood plasma and serum samples. Analytical Biochemistry. 414: 99-102. PMID 21371419 DOI: 10.1016/J.Ab.2011.02.039  0.542
2011 Stöckel J, Jacobs JM, Elvitigala TR, Liberton M, Welsh EA, Polpitiya AD, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB. Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142. Plos One. 6: e16680. PMID 21364985 DOI: 10.1371/Journal.Pone.0016680  0.323
2011 Belov ME, Prasad S, Prior DC, Danielson WF, Weitz K, Ibrahim YM, Smith RD. Pulsed multiple reaction monitoring approach to enhancing sensitivity of a tandem quadrupole mass spectrometer. Analytical Chemistry. 83: 2162-71. PMID 21344863 DOI: 10.1021/Ac103006B  0.407
2011 Du X, Chowdhury SM, Manes NP, Wu S, Mayer MU, Adkins JN, Anderson GA, Smith RD. Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry. Journal of Proteome Research. 10: 923-31. PMID 21175198 DOI: 10.1021/Pr100848A  0.402
2011 Huang X, Tolmachev AV, Shen Y, Liu M, Huang L, Zhang Z, Anderson GA, Smith RD, Chan WC, Hinrichs SH, Fu K, Ding SJ. UNiquant, a program for quantitative proteomics analysis using stable isotope labeling. Journal of Proteome Research. 10: 1228-37. PMID 21158445 DOI: 10.1021/Pr1010058  0.311
2011 Brown RN, Romine MF, Schepmoes AA, Smith RD, Lipton MS. Mapping the subcellular proteome of Shewanella oneidensis MR-1 using sarkosyl-based fractionation and LC-MS/MS protein identification. Journal of Proteome Research. 9: 4454-63. PMID 20690604 DOI: 10.1021/Pr100215H  0.395
2011 Shvartsburg AA, Prior DC, Tang K, Smith RD. High-resolution differential ion mobility separations using planar analyzers at elevated dispersion fields. Analytical Chemistry. 82: 7649-55. PMID 20666414 DOI: 10.1021/Ac101413K  0.407
2011 López-Ferrer D, Petritis K, Robinson EW, Hixson KK, Tian Z, Lee JH, Lee SW, Tolić N, Weitz KK, Belov ME, Smith RD, Pasa-Tolić L. Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics. Molecular & Cellular Proteomics : McP. 10: M110.001479. PMID 20627868 DOI: 10.1074/Mcp.M110.001479  0.397
2011 Hossain M, Kaleta DT, Robinson EW, Liu T, Zhao R, Page JS, Kelly RT, Moore RJ, Tang K, Camp DG, Qian WJ, Smith RD. Enhanced sensitivity for selected reaction monitoring mass spectrometry-based targeted proteomics using a dual stage electrodynamic ion funnel interface. Molecular & Cellular Proteomics : McP. 10: M000062-MCP201. PMID 20410378 DOI: 10.1074/Mcp.M000062-Mcp201  0.453
2011 Johnson PV, Hodyss R, Tang K, Brinckerhoff WB, Smith RD. The laser ablation ion funnel: Sampling for in situ mass spectrometry on Mars Planetary and Space Science. 59: 387-393. DOI: 10.1016/J.Pss.2011.01.004  0.363
2011 Shvartsburg AA, Isaac G, Leveque N, Smith RD, Metz TO. Erratum to: Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry Journal of the American Society For Mass Spectrometry. 22: 1156-1156. DOI: 10.1007/S13361-011-0156-2  0.598
2010 Karpievitch YV, Polpitiya AD, Anderson GA, Smith RD, Dabney AR. Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects. The Annals of Applied Statistics. 4: 1797-1823. PMID 21593992 DOI: 10.1214/10-Aoas341  0.383
2010 Shvartsburg AA, Smith RD. Ultrahigh-resolution differential ion mobility spectrometry using extended separation times. Analytical Chemistry. 83: 23-9. PMID 21117630 DOI: 10.1021/Ac102689P  0.366
2010 Angel TE, Luft BJ, Yang X, Nicora CD, Camp DG, Jacobs JM, Smith RD. Proteome analysis of Borrelia burgdorferi response to environmental change. Plos One. 5: e13800. PMID 21072190 DOI: 10.1371/Journal.Pone.0013800  0.308
2010 Marginean I, Page JS, Tolmachev AV, Tang K, Smith RD. Achieving 50% ionization efficiency in subambient pressure ionization with nanoelectrospray. Analytical Chemistry. 82: 9344-9. PMID 21028835 DOI: 10.1021/Ac1019123  0.351
2010 Tian Z, Zhao R, Tolić N, Moore RJ, Stenoien DL, Robinson EW, Smith RD, Paša-Tolić L. Two-dimensional liquid chromatography system for online top-down mass spectrometry. Proteomics. 10: 3610-20. PMID 20879039 DOI: 10.1002/Pmic.201000367  0.362
2010 Buchko GW, Niemann G, Baker ES, Belov ME, Smith RD, Heffron F, Adkins JN, McDermott JE. A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins. Molecular Biosystems. 6: 2448-58. PMID 20877914 DOI: 10.1039/C0Mb00097C  0.576
2010 Jung HJ, Purvine SO, Kim H, Petyuk VA, Hyung SW, Monroe ME, Mun DG, Kim KC, Park JM, Kim SJ, Tolic N, Slysz GW, Moore RJ, Zhao R, Adkins JN, ... ... Smith RD, et al. Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data. Analytical Chemistry. 82: 8510-8. PMID 20863060 DOI: 10.1021/Ac101388B  0.418
2010 Shvartsburg AA, Creese AJ, Smith RD, Cooper HJ. Separation of peptide isomers with variant modified sites by high-resolution differential ion mobility spectrometry. Analytical Chemistry. 82: 8327-34. PMID 20843012 DOI: 10.1021/Ac101878A  0.453
2010 Shvartsburg AA, Clemmer DE, Smith RD. Isotopic effect on ion mobility and separation of isotopomers by high-field ion mobility spectrometry. Analytical Chemistry. 82: 8047-51. PMID 20815340 DOI: 10.1021/Ac101992D  0.407
2010 Zhou JY, Schepmoes AA, Zhang X, Moore RJ, Monroe ME, Lee JH, Camp DG, Smith RD, Qian WJ. Improved LC-MS/MS spectral counting statistics by recovering low-scoring spectra matched to confidently identified peptide sequences. Journal of Proteome Research. 9: 5698-704. PMID 20812748 DOI: 10.1021/Pr100508P  0.408
2010 Qian WJ, Petritis BO, Kaushal A, Finnerty CC, Jeschke MG, Monroe ME, Moore RJ, Schepmoes AA, Xiao W, Moldawer LL, Davis RW, Tompkins RG, Herndon DN, Camp DG, Smith RD, et al. Plasma proteome response to severe burn injury revealed by 18O-labeled "universal" reference-based quantitative proteomics. Journal of Proteome Research. 9: 4779-89. PMID 20698492 DOI: 10.1021/Pr1005026  0.317
2010 Liu M, Hou J, Huang L, Huang X, Heibeck TH, Zhao R, Pasa-Tolic L, Smith RD, Li Y, Fu K, Zhang Z, Hinrichs SH, Ding SJ. Site-specific proteomics approach for study protein S-nitrosylation. Analytical Chemistry. 82: 7160-8. PMID 20687582 DOI: 10.1021/Ac100569D  0.323
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  0.653
2010 Sun X, Kelly RT, Tang K, Smith RD. Ultrasensitive nanoelectrospray ionization-mass spectrometry using poly(dimethylsiloxane) microchips with monolithically integrated emitters. The Analyst. 135: 2296-302. PMID 20617264 DOI: 10.1039/C0An00253D  0.387
2010 Gupta N, Hixson KK, Culley DE, Smith RD, Pevzner PA. Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry. Proteomics. 10: 2833-44. PMID 20597098 DOI: 10.1002/Pmic.200900821  0.386
2010 Ibrahim YM, Prior DC, Baker ES, Smith RD, Belov ME. Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation-Tandem Time-of-Flight Mass Spectrometry Approach. International Journal of Mass Spectrometry. 293: 34-44. PMID 20596241 DOI: 10.1016/J.Ijms.2010.03.009  0.664
2010 Shen Y, Tolić N, Purvine SO, Smith RD. Identification of disulfide bonds in protein proteolytic degradation products using de novo-protein unique sequence tags approach. Journal of Proteome Research. 9: 4053-60. PMID 20590115 DOI: 10.1021/Pr1002559  0.389
2010 Sorensen CM, Ding J, Zhang Q, Alquier T, Zhao R, Mueller PW, Smith RD, Metz TO. Perturbations in the lipid profile of individuals with newly diagnosed type 1 diabetes mellitus: lipidomics analysis of a Diabetes Antibody Standardization Program sample subset. Clinical Biochemistry. 43: 948-56. PMID 20519132 DOI: 10.1016/J.Clinbiochem.2010.04.075  0.56
2010 Shah AR, Agarwal K, Baker ES, Singhal M, Mayampurath AM, Ibrahim YM, Kangas LJ, Monroe ME, Zhao R, Belov ME, Anderson GA, Smith RD. Machine learning based prediction for peptide drift times in ion mobility spectrometry. Bioinformatics (Oxford, England). 26: 1601-7. PMID 20495001 DOI: 10.1093/Bioinformatics/Btq245  0.637
2010 Alpert AJ, Petritis K, Kangas L, Smith RD, Mechtler K, Mitulović G, Mohammed S, Heck AJ. Peptide orientation affects selectivity in ion-exchange chromatography. Analytical Chemistry. 82: 5253-9. PMID 20481592 DOI: 10.1021/Ac100651K  0.308
2010 Rana GS, York TP, Edmiston JS, Zedler BK, Pounds JG, Adkins JN, Varnum SM, Smith RD, Liu Z, Li G, Webb BT, Murrelle EL, Flora JW. Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD). Analytical and Bioanalytical Chemistry. 397: 1809-19. PMID 20442989 DOI: 10.1007/S00216-010-3742-4  0.342
2010 Lourette N, Smallwood H, Wu S, Robinson EW, Squier TC, Smith RD, Pasa-Tolić L. A top-down LC-FTICR MS-based strategy for characterizing oxidized calmodulin in activated macrophages. Journal of the American Society For Mass Spectrometry. 21: 930-9. PMID 20417115 DOI: 10.1016/J.Jasms.2010.02.027  0.392
2010 Zhang H, Brown RN, Qian WJ, Monroe ME, Purvine SO, Moore RJ, Gritsenko MA, Shi L, Romine MF, Fredrickson JK, Pasa-Tolić L, Smith RD, Lipton MS. Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling. Journal of Proteome Research. 9: 2160-9. PMID 20380418 DOI: 10.1021/Pr9009113  0.337
2010 Shen Y, Liu T, Toli? N, Petritis BO, Zhao R, Moore RJ, Purvine SO, Camp DG, Smith RD. Strategy for degradomic-peptidomic analysis of human blood plasma. Journal of Proteome Research. 9: 2339-46. PMID 20377236 DOI: 10.1021/Pr901083M  0.368
2010 Shvartsburg AA, Danielson WF, Smith RD. High-resolution differential ion mobility separations using helium-rich gases. Analytical Chemistry. 82: 2456-62. PMID 20151640 DOI: 10.1021/Ac902852A  0.448
2010 Zhang X, Monroe ME, Chen B, Chin MH, Heibeck TH, Schepmoes AA, Yang F, Petritis BO, Camp DG, Pounds JG, Jacobs JM, Smith DJ, Bigelow DJ, Smith RD, Qian WJ. Endogenous 3,4-dihydroxyphenylalanine and dopaquinone modifications on protein tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical. Molecular & Cellular Proteomics : McP. 9: 1199-208. PMID 20124354 DOI: 10.1074/Mcp.M900321-Mcp200  0.302
2010 Diamond DL, Syder AJ, Jacobs JM, Sorensen CM, Walters KA, Proll SC, McDermott JE, Gritsenko MA, Zhang Q, Zhao R, Metz TO, Camp DG, Waters KM, Smith RD, Rice CM, et al. Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics. Plos Pathogens. 6: e1000719. PMID 20062526 DOI: 10.1371/Journal.Ppat.1000719  0.537
2010 Petyuk VA, Mayampurath AM, Monroe ME, Polpitiya AD, Purvine SO, Anderson GA, Camp DG, Smith RD. DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets. Molecular & Cellular Proteomics : McP. 9: 486-96. PMID 20019053 DOI: 10.1074/Mcp.M900217-Mcp200  0.425
2010 Adkins JN, Mottaz H, Metz TO, Ansong C, Manes NP, Smith RD, Heffron F. Performing comparative peptidomics analyses of Salmonella from different growth conditions. Methods in Molecular Biology (Clifton, N.J.). 615: 13-27. PMID 20013197 DOI: 10.1007/978-1-60761-535-4_2  0.605
2010 Baker ES, Livesay EA, Orton DJ, Moore RJ, Danielson WF, Prior DC, Ibrahim YM, LaMarche BL, Mayampurath AM, Schepmoes AA, Hopkins DF, Tang K, Smith RD, Belov ME. An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. Journal of Proteome Research. 9: 997-1006. PMID 20000344 DOI: 10.1021/Pr900888B  0.658
2010 Kim J, Kim BC, Lopez-Ferrer D, Petritis K, Smith RD. Nanobiocatalysis for protein digestion in proteomic analysis. Proteomics. 10: 687-99. PMID 19953546 DOI: 10.1002/Pmic.200900519  0.329
2010 Shvartsburg AA, Tang K, Smith RD. Differential ion mobility separations of peptides with resolving power exceeding 50. Analytical Chemistry. 82: 32-5. PMID 19938817 DOI: 10.1021/Ac902133N  0.374
2010 Petyuk VA, Qian WJ, Smith RD, Smith DJ. Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry. Methods (San Diego, Calif.). 50: 77-84. PMID 19654045 DOI: 10.1016/J.Ymeth.2009.07.009  0.352
2010 Kelly RT, Tolmachev AV, Page JS, Tang K, Smith RD. The ion funnel: theory, implementations, and applications. Mass Spectrometry Reviews. 29: 294-312. PMID 19391099 DOI: 10.1002/Mas.20232  0.358
2010 Smith RD. Advanced mass spectrometric methods for the rapid and quantitative characterization of proteomes. Comparative and Functional Genomics. 3: 143-50. PMID 18628837 DOI: 10.1002/cfg.159  0.393
2009 Tolmachev AV, Robinson EW, Wu S, Paša-Tolić L, Smith RD. FT-ICR MS optimization for the analysis of intact proteins. International Journal of Mass Spectrometry. 281: 32-38. PMID 20473360 DOI: 10.1016/J.Ijms.2008.10.010  0.438
2009 Page JS, Marginean I, Baker ES, Kelly RT, Tang K, Smith RD. Biases in ion transmission through an electrospray ionization-mass spectrometry capillary inlet. Journal of the American Society For Mass Spectrometry. 20: 2265-72. PMID 19815425 DOI: 10.1016/J.Jasms.2009.08.018  0.621
2009 Prasad S, Tang K, Manura D, Papanastasiou D, Smith RD. Simulation of ion motion in FAIMS through combined use of SIMION and modified SDS. Analytical Chemistry. 81: 8749-57. PMID 19785446 DOI: 10.1021/Ac900880V  0.387
2009 Zhou JY, Petritis BO, Petritis K, Norbeck AD, Weitz KK, Moore RJ, Camp DG, Kulkarni RN, Smith RD, Qian WJ. Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome. Journal of Proteome Research. 8: 5387-95. PMID 19722698 DOI: 10.1021/Pr900564F  0.415
2009 Alquier T, Peyot ML, Latour MG, Kebede M, Sorensen CM, Gesta S, Ronald Kahn C, Smith RD, Jetton TL, Metz TO, Prentki M, Poitout V. Deletion of GPR40 impairs glucose-induced insulin secretion in vivo in mice without affecting intracellular fuel metabolism in islets. Diabetes. 58: 2607-15. PMID 19720802 DOI: 10.2337/Db09-0362  0.517
2009 Shvartsburg AA, Tang K, Smith RD, Holden M, Rush M, Thompson A, Toutoungi D. Ultrafast differential ion mobility spectrometry at extreme electric fields coupled to mass spectrometry Analytical Chemistry. 81: 8048-8053. PMID 19708673 DOI: 10.1021/Ac901479E  0.409
2009 Kelly RT, Page JS, Marginean I, Tang K, Smith RD. Dilution-free analysis from picoliter droplets by nano-electrospray ionization mass spectrometry. Angewandte Chemie (International Ed. in English). 48: 6832-5. PMID 19688798 DOI: 10.1002/Anie.200902501  0.332
2009 Mabrouki R, Kelly RT, Prior DC, Shvartsburg AA, Tang K, Smith RD. Improving FAIMS sensitivity using a planar geometry with slit interfaces. Journal of the American Society For Mass Spectrometry. 20: 1768-74. PMID 19616967 DOI: 10.1016/J.Jasms.2009.05.019  0.428
2009 Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR. Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. Bioinformatics (Oxford, England). 25: 2573-80. PMID 19602524 DOI: 10.1093/Bioinformatics/Btp426  0.358
2009 Shvartsburg AA, Smith RD, Wilks A, Koehl A, Ruiz-Alonso D, Boyle B. Ultrafast differential ion mobility spectrometry at extreme electric fields in multichannel microchips. Analytical Chemistry. 81: 6489-95. PMID 19583243 DOI: 10.1021/Ac900892U  0.343
2009 Pez-Ferrer DL, Hixson KK, Smallwood H, Squier TC, Petritis K, Smith RD. Evaluation of a high-intensity focused ultrasound-immobilized trypsin digestion and 18O-labeling method for quantitative proteomics Analytical Chemistry. 81: 6272-6277. PMID 19555078 DOI: 10.1021/Ac802540S  0.312
2009 Karpievitch Y, Stanley J, Taverner T, Huang J, Adkins JN, Ansong C, Heffron F, Metz TO, Qian WJ, Yoon H, Smith RD, Dabney AR. A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics (Oxford, England). 25: 2028-34. PMID 19535538 DOI: 10.1093/Bioinformatics/Btp362  0.619
2009 Heibeck TH, Ding SJ, Opresko LK, Zhao R, Schepmoes AA, Yang F, Tolmachev AV, Monroe ME, Camp DG, Smith RD, Wiley HS, Qian WJ. An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells. Journal of Proteome Research. 8: 3852-61. PMID 19534553 DOI: 10.1021/Pr900044C  0.31
2009 Chowdhury SM, Du X, Toli? N, Wu S, Moore RJ, Mayer MU, Smith RD, Adkins JN. Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry. Analytical Chemistry. 81: 5524-32. PMID 19496583 DOI: 10.1021/Ac900853K  0.405
2009 Park CC, Petyuk VA, Qian WJ, Smith RD, Smith DJ. Dual spatial maps of transcript and protein abundance in the mouse brain. Expert Review of Proteomics. 6: 243-9. PMID 19489697 DOI: 10.1586/Epr.09.46  0.312
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  0.692
2009 Wu S, Yang F, Zhao R, Tolić N, Robinson EW, Camp DG, Smith RD, Pasa-Tolić L. Integrated workflow for characterizing intact phosphoproteins from complex mixtures. Analytical Chemistry. 81: 4210-9. PMID 19425582 DOI: 10.1021/Ac802487Q  0.416
2009 Yang F, Wu S, Stenoien DL, Zhao R, Monroe ME, Gritsenko MA, Purvine SO, Polpitiya AD, Tolić N, Zhang Q, Norbeck AD, Orton DJ, Moore RJ, Tang K, Anderson GA, ... ... Smith RD, et al. Combined pulsed-Q dissociation and electron transfer dissociation for identification and quantification of iTRAQ-labeled phosphopeptides. Analytical Chemistry. 81: 4137-43. PMID 19371082 DOI: 10.1021/Ac802605M  0.412
2009 Shvartsburg AA, Noskov SY, Purves RW, Smith RD. Pendular proteins in gases and new avenues for characterization of macromolecules by ion mobility spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 106: 6495-500. PMID 19351899 DOI: 10.1073/Pnas.0812318106  0.38
2009 Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD. Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. Bmc Bioinformatics. 10: 87. PMID 19292916 DOI: 10.1186/1471-2105-10-87  0.354
2009 Kim BC, Lopez-Ferrer D, Lee SM, Ahn HK, Nair S, Kim SH, Kim BS, Petritis K, Camp DG, Grate JW, Smith RD, Koo YM, Gu MB, Kim J. Highly stable trypsin-aggregate coatings on polymer nanofibers for repeated protein digestion Proteomics. 9: 1893-1900. PMID 19288524 DOI: 10.1002/Pmic.200800591  0.343
2009 Shvartsburg AA, Tang K, Smith RD. Two-dimensional ion mobility analyses of proteins and peptides. Methods in Molecular Biology (Clifton, N.J.). 492: 417-45. PMID 19241049 DOI: 10.1007/978-1-59745-493-3_26  0.437
2009 Zhao R, Ding SJ, Shen Y, Camp DG, Livesay EA, Udseth H, Smith RD. Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 877: 663-70. PMID 19217835 DOI: 10.1016/J.Jchromb.2008.12.068  0.378
2009 Wu S, Lourette NM, Tolić N, Zhao R, Robinson EW, Tolmachev AV, Smith RD, Pasa-Tolić L. An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications. Journal of Proteome Research. 8: 1347-57. PMID 19206473 DOI: 10.1021/Pr800720D  0.415
2009 Chowdhury SM, Shi L, Yoon H, Ansong C, Rommereim LM, Norbeck AD, Auberry KJ, Moore RJ, Adkins JN, Heffron F, Smith RD. A method for investigating protein-protein interactions related to salmonella typhimurium pathogenesis. Journal of Proteome Research. 8: 1504-14. PMID 19206470 DOI: 10.1021/Pr800865D  0.317
2009 Marginean I, Kelly RT, Moore RJ, Prior DC, LaMarche BL, Tang K, Smith RD. Selection of the optimum electrospray voltage for gradient elution LC-MS measurements. Journal of the American Society For Mass Spectrometry. 20: 682-8. PMID 19196520 DOI: 10.1016/J.Jasms.2008.12.004  0.35
2009 Zhang Q, Ames JM, Smith RD, Baynes JW, Metz TO. A perspective on the Maillard reaction and the analysis of protein glycation by mass spectrometry: probing the pathogenesis of chronic disease. Journal of Proteome Research. 8: 754-69. PMID 19093874 DOI: 10.1021/Pr800858H  0.689
2009 Qian WJ, Liu T, Petyuk VA, Gritsenko MA, Petritis BO, Polpitiya AD, Kaushal A, Xiao W, Finnerty CC, Jeschke MG, Jaitly N, Monroe ME, Moore RJ, Moldawer LL, Davis RW, ... ... Smith RD, et al. Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample. Journal of Proteome Research. 8: 290-9. PMID 19053531 DOI: 10.1021/Pr800467R  0.322
2009 Shvartsburg AA, Smith RD. Fundamentals of traveling wave ion mobility spectrometry. Analytical Chemistry. 80: 9689-99. PMID 18986171 DOI: 10.1021/Ac8016295  0.352
2009 Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF, Carlson CA, Smith RD, Giovanonni SJ. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. The Isme Journal. 3: 93-105. PMID 18769456 DOI: 10.1038/Ismej.2008.83  0.366
2009 Zhang Q, Ames JM, Smith RD, Baynes JW, Metz TO. A perspective on the maillard reaction and the analysis of protein glycation by mass spectrometry Journal of Proteome Research. 8: 754-769. DOI: 10.1021/Pr80085Bh  0.705
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  0.684
2008 Metz TO, Page JS, Baker ES, Tang K, Ding J, Shen Y, Smith RD. High Resolution Separations and Improved Ion Production and Transmission in Metabolomics. Trends in Analytical Chemistry : Trac. 27: 205-214. PMID 19255623 DOI: 10.1016/J.Trac.2007.11.003  0.769
2008 Rodland KD, Adkins JN, Ansong C, Chowdhury S, Manes NP, Shi L, Yoon H, Smith RD, Heffron F. Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella. Future Microbiology. 3: 625-34. PMID 19072180 DOI: 10.2217/17460913.3.6.625  0.367
2008 Zhang Q, Schepmoes AA, Brock JW, Wu S, Moore RJ, Purvine SO, Baynes JW, Smith RD, Metz TO. Improved methods for the enrichment and analysis of glycated peptides. Analytical Chemistry. 80: 9822-9. PMID 18989935 DOI: 10.1021/Ac801704J  0.726
2008 Tolmachev AV, Monroe ME, Purvine SO, Moore RJ, Jaitly N, Adkins JN, Anderson GA, Smith RD. Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments. Analytical Chemistry. 80: 8514-25. PMID 18855412 DOI: 10.1021/Ac801376G  0.435
2008 Ding SJ, Wang Y, Jacobs JM, Qian WJ, Yang F, Tolmachev AV, Du X, Wang W, Moore RJ, Monroe ME, Purvine SO, Waters K, Heibeck TH, Adkins JN, Camp DG, ... ... Smith RD, et al. Quantitative phosphoproteome analysis of lysophosphatidic acid induced chemotaxis applying dual-step (18)O labeling coupled with immobilized metal-ion affinity chromatography. Journal of Proteome Research. 7: 4215-24. PMID 18785766 DOI: 10.1021/Pr7007785  0.424
2008 Shen Y, Tolić N, Hixson KK, Purvine SO, Anderson GA, Smith RD. De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins Analytical Chemistry. 80: 7742-7754. PMID 18783246 DOI: 10.1021/Ac801123P  0.321
2008 Zhang Q, Petyuk VA, Schepmoes AA, Orton DJ, Monroe ME, Yang F, Smith RD, Metz TO. Analysis of non-enzymatically glycated peptides: neutral-loss-triggered MS(3) versus multi-stage activation tandem mass spectrometry. Rapid Communications in Mass Spectrometry : Rcm. 22: 3027-34. PMID 18763275 DOI: 10.1002/Rcm.3703  0.623
2008 Robinson EW, Shvartsburg AA, Tang K, Smith RD. Control of ion distortion in field asymmetric waveform ion mobility spectrometry via variation of dispersion field and gas temperature. Analytical Chemistry. 80: 7508-15. PMID 18729473 DOI: 10.1021/Ac800655D  0.335
2008 López-Ferrer D, Heibeck TH, Petritis K, Hixson KK, Qian W, Monroe ME, Mayampurath A, Moore RJ, Belov ME, Camp DG, Smith RD. Rapid sample processing for LC-MS-based quantitative proteomics using high intensity focused ultrasound. Journal of Proteome Research. 7: 3860-7. PMID 18686986 DOI: 10.1021/Pr800161X  0.412
2008 Marginean I, Kelly RT, Prior DC, LaMarche BL, Tang K, Smith RD. Analytical characterization of the electrospray ion source in the nanoflow regime. Analytical Chemistry. 80: 6573-9. PMID 18661954 DOI: 10.1021/Ac800683S  0.384
2008 Qian WJ, Kaleta DT, Petritis BO, Jiang H, Liu T, Zhang X, Mottaz HM, Varnum SM, Camp DG, Huang L, Fang X, Zhang WW, Smith RD. Enhanced detection of low abundance human plasma proteins using a tandem IgY12-SuperMix immunoaffinity separation strategy. Molecular & Cellular Proteomics : McP. 7: 1963-73. PMID 18632595 DOI: 10.1074/Mcp.M800008-Mcp200  0.366
2008 López-Ferrer D, Petritis K, Hixson KK, Heibeck TH, Moore RJ, Belov ME, Camp DG, Smith RD. Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: Proteomics on the fly Journal of Proteome Research. 7: 3276-3281. PMID 18605748 DOI: 10.1021/Pr7008077  0.36
2008 Shvartsburg AA, Smith RD. Optimum waveforms for differential ion mobility spectrometry (FAIMS). Journal of the American Society For Mass Spectrometry. 19: 1286-95. PMID 18585054 DOI: 10.1016/J.Jasms.2008.05.008  0.361
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  0.712
2008 Shen Y, Hixson KK, Tolić N, Camp DG, Purvine SO, Moore RJ, Smith RD. Mass spectrometry analysis of proteome-wide proteolytic post-translational degradation of proteins Analytical Chemistry. 80: 5819-5828. PMID 18578501 DOI: 10.1021/Ac800077W  0.367
2008 Petyuk VA, Qian WJ, Hinault C, Gritsenko MA, Singhal M, Monroe ME, Camp DG, Kulkarni RN, Smith RD. Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues. Journal of Proteome Research. 7: 3114-26. PMID 18570455 DOI: 10.1021/Pr800205B  0.36
2008 Ibrahim YM, Belov ME, Liyu AV, Smith RD. Automated gain control ion funnel trap for orthogonal time-of-flight mass spectrometry. Analytical Chemistry. 80: 5367-76. PMID 18512944 DOI: 10.1021/Ac8003488  0.454
2008 Ding J, Sorensen CM, Jaitly N, Jiang H, Orton DJ, Monroe ME, Moore RJ, Smith RD, Metz TO. Application of the accurate mass and time tag approach in studies of the human blood lipidome. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 871: 243-52. PMID 18502191 DOI: 10.1016/J.Jchromb.2008.04.040  0.607
2008 Du X, Callister SJ, Manes NP, Adkins JN, Alexandridis RA, Zeng X, Roh JH, Smith WE, Donohue TJ, Kaplan S, Smith RD, Lipton MS. A computational strategy to analyze label-free temporal bottom-up proteomics data. Journal of Proteome Research. 7: 2595-604. PMID 18442284 DOI: 10.1021/Pr0704837  0.346
2008 Monroe ME, Shaw JL, Daly DS, Adkins JN, Smith RD. MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. Computational Biology and Chemistry. 32: 215-7. PMID 18440872 DOI: 10.1016/J.Compbiolchem.2008.02.006  0.413
2008 Du X, Yang F, Manes NP, Stenoien DL, Monroe ME, Adkins JN, States DJ, Purvine SO, Camp DG, Smith RD. Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications. Journal of Proteome Research. 7: 2195-203. PMID 18422353 DOI: 10.1021/Pr070510T  0.328
2008 Kelly RT, Tang K, Irimia D, Toner M, Smith RD. Elastomeric microchip electrospray emitter for stable cone-jet mode operation in the nanoflow regime. Analytical Chemistry. 80: 3824-31. PMID 18419138 DOI: 10.1021/Ac8000786  0.369
2008 Ham BM, Yang F, Jayachandran H, Jaitly N, Monroe ME, Gritsenko MA, Livesay EA, Zhao R, Purvine SO, Orton D, Adkins JN, Camp DG, Rossie S, Smith RD. The influence of sample preparation and replicate analyses on HeLa Cell phosphoproteome coverage. Journal of Proteome Research. 7: 2215-21. PMID 18412383 DOI: 10.1021/Pr700575M  0.411
2008 Zhang Q, Tang N, Schepmoes AA, Phillips LS, Smith RD, Metz TO. Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes. Journal of Proteome Research. 7: 2025-32. PMID 18396901 DOI: 10.1021/Pr700763R  0.573
2008 Ansong C, Purvine SO, Adkins JN, Lipton MS, Smith RD. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Briefings in Functional Genomics & Proteomics. 7: 50-62. PMID 18334489 DOI: 10.1093/Bfgp/Eln010  0.301
2008 Pounds JG, Flora JW, Adkins JN, Lee KM, Rana GS, Sengupta T, Smith RD, McKinney WJ. Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 864: 95-101. PMID 18313996 DOI: 10.1016/J.Jchromb.2008.01.044  0.426
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  0.673
2008 Mayampurath AM, Jaitly N, Purvine SO, Monroe ME, Auberry KJ, Adkins JN, Smith RD. DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics (Oxford, England). 24: 1021-3. PMID 18304935 DOI: 10.1093/Bioinformatics/Btn063  0.352
2008 Tolmachev AV, Robinson EW, Wu S, Kang H, Lourette NM, Pasa-Tolić L, Smith RD. Trapped-ion cell with improved DC potential harmonicity for FT-ICR MS. Journal of the American Society For Mass Spectrometry. 19: 586-97. PMID 18296061 DOI: 10.1016/J.Jasms.2008.01.006  0.4
2008 Shen Y, Tolić N, Hixson KK, Purvine SO, Pasa-Tolić L, Qian WJ, Adkins JN, Moore RJ, Smith RD. Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags. Analytical Chemistry. 80: 1871-82. PMID 18271604 DOI: 10.1021/Ac702328X  0.405
2008 Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, ... ... Smith RD, et al. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26: 164-7. PMID 18259167 DOI: 10.1038/Nbt0208-164  0.507
2008 Page JS, Tang K, Kelly RT, Smith RD. Subambient pressure ionization with nanoelectrospray source and interface for improved sensitivity in mass spectrometry. Analytical Chemistry. 80: 1800-5. PMID 18237189 DOI: 10.1021/Ac702354B  0.39
2008 Baker ES, Tang K, Danielson WF, Prior DC, Smith RD. Simultaneous fragmentation of multiple ions using IMS drift time dependent collision energies. Journal of the American Society For Mass Spectrometry. 19: 411-9. PMID 18226544 DOI: 10.1016/J.Jasms.2007.11.018  0.626
2008 Manes NP, Estep RD, Mottaz HM, Moore RJ, Clauss TR, Monroe ME, Du X, Adkins JN, Wong SW, Smith RD. Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions. Journal of Proteome Research. 7: 960-8. PMID 18205298 DOI: 10.1021/Pr070432+  0.405
2008 Chin MH, Qian WJ, Wang H, Petyuk VA, Bloom JS, Sforza DM, La?an G, Liu D, Khan AH, Cantor RM, Bigelow DJ, Melega WP, Camp DG, Smith RD, Smith DJ. Mitochondrial dysfunction, oxidative stress, and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's disease. Journal of Proteome Research. 7: 666-77. PMID 18173235 DOI: 10.1021/Pr070546L  0.301
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  0.663
2008 Jacobs JM, Waters KM, Kathmann LE, Camp DG, Wiley HS, Smith RD, Thrall BD. The mammary epithelial cell secretome and its regulation by signal transduction pathways. Journal of Proteome Research. 7: 558-69. PMID 18166007 DOI: 10.1021/Pr0704377  0.344
2008 Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD. Proteomics analysis of the causative agent of typhoid fever. Journal of Proteome Research. 7: 546-57. PMID 18166006 DOI: 10.1021/Pr070434U  0.322
2008 Petyuk VA, Jaitly N, Moore RJ, Ding J, Metz TO, Tang K, Monroe ME, Tolmachev AV, Adkins JN, Belov ME, Dabney AR, Qian WJ, Camp DG, Smith RD. Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content. Analytical Chemistry. 80: 693-706. PMID 18163597 DOI: 10.1021/Ac701863D  0.609
2008 Metz TO, Qian WJ, Jacobs JM, Gritsenko MA, Moore RJ, Polpitiya AD, Monroe ME, Camp DG, Mueller PW, Smith RD. Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset. Journal of Proteome Research. 7: 698-707. PMID 18092746 DOI: 10.1021/Pr700606W  0.586
2008 Rodriguez J, Gupta N, Smith RD, Pevzner PA. Does trypsin cut before proline? Journal of Proteome Research. 7: 300-5. PMID 18067249 DOI: 10.1021/Pr0705035  0.371
2008 Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. Clustering millions of tandem mass spectra. Journal of Proteome Research. 7: 113-22. PMID 18067247 DOI: 10.1021/Pr070361E  0.377
2008 Huang Y, Tseng GC, Yuan S, Pasa-Tolic L, Lipton MS, Smith RD, Wysocki VH. A data-mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns. Journal of Proteome Research. 7: 70-9. PMID 18052120 DOI: 10.1021/Pr070106U  0.4
2008 Livesay EA, Tang K, Taylor BK, Buschbach MA, Hopkins DF, LaMarche BL, Zhao R, Shen Y, Orton DJ, Moore RJ, Kelly RT, Udseth HR, Smith RD. Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses. Analytical Chemistry. 80: 294-302. PMID 18044960 DOI: 10.1021/Ac701727R  0.372
2008 Kelly RT, Page JS, Zhao R, Qian WJ, Mottaz HM, Tang K, Smith RD. Capillary-based multi nanoelectrospray emitters: improvements in ion transmission efficiency and implementation with capillary reversed-phase LC-ESI-MS. Analytical Chemistry. 80: 143-9. PMID 18044958 DOI: 10.1021/Ac701647S  0.415
2007 Metz TO, Zhang Q, Page JS, Shen Y, Callister SJ, Jacobs JM, Smith RD. The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery. Biomarkers in Medicine. 1: 159-185. PMID 19177179 DOI: 10.2217/17520363.1.1.159  0.628
2007 Kim J, Petritis K, Shen Y, Camp DG, Moore RJ, Smith RD. Phosphopeptide elution times in reversed-phase liquid chromatography. Journal of Chromatography. A. 1172: 9-18. PMID 17935722 DOI: 10.1016/J.Chroma.2007.09.032  0.303
2007 Yang F, Jaitly N, Jayachandran H, Luo Q, Monroe ME, Du X, Gritsenko MA, Zhang R, Anderson DJ, Purvine SO, Adkins JN, Moore RJ, Mottaz HM, Ding SJ, Lipton MS, ... ... Smith RD, et al. Applying a targeted label-free approach using LC-MS AMT tags to evaluate changes in protein phosphorylation following phosphatase inhibition. Journal of Proteome Research. 6: 4489-97. PMID 17929957 DOI: 10.1021/Pr070068E  0.343
2007 Marginean I, Kelly RT, Page JS, Tang K, Smith RD. Electrospray characteristic curves: in pursuit of improved performance in the nanoflow regime. Analytical Chemistry. 79: 8030-6. PMID 17896826 DOI: 10.1021/Ac0707986  0.326
2007 Ibrahim Y, Belov ME, Tolmachev AV, Prior DC, Smith RD. Ion funnel trap interface for orthogonal time-of-flight mass spectrometry. Analytical Chemistry. 79: 7845-52. PMID 17850113 DOI: 10.1021/Ac071091M  0.396
2007 Shvartsburg AA, Smith RD. Scaling of the resolving power and sensitivity for planar FAIMS and mobility-based discrimination in flow- and field-driven analyzers. Journal of the American Society For Mass Spectrometry. 18: 1672-81. PMID 17723907 DOI: 10.1016/J.Jasms.2007.06.013  0.349
2007 Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Research. 17: 1362-77. PMID 17690205 DOI: 10.1101/Gr.6427907  0.374
2007 Liu T, Belov ME, Jaitly N, Qian WJ, Smith RD. Accurate mass measurements in proteomics. Chemical Reviews. 107: 3621-53. PMID 17649984 DOI: 10.1021/Cr068288J  0.375
2007 Ding J, Sorensen CM, Zhang Q, Jiang H, Jaitly N, Livesay EA, Shen Y, Smith RD, Metz TO. Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profiling. Analytical Chemistry. 79: 6081-93. PMID 17636878 DOI: 10.1021/Ac070080Q  0.626
2007 Page JS, Kelly RT, Tang K, Smith RD. Ionization and transmission efficiency in an electrospray ionization-mass spectrometry interface. Journal of the American Society For Mass Spectrometry. 18: 1582-90. PMID 17627841 DOI: 10.1016/J.Jasms.2007.05.018  0.386
2007 Monroe ME, Tolić N, Jaitly N, Shaw JL, Adkins JN, Smith RD. VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics (Oxford, England). 23: 2021-3. PMID 17545182 DOI: 10.1093/Bioinformatics/Btm281  0.35
2007 Kang H, Pasa-Tolić L, Smith RD. Targeted tandem mass spectrometry for high-throughput comparative proteomics employing NanoLC-FTICR MS with external ion dissociation. Journal of the American Society For Mass Spectrometry. 18: 1332-43. PMID 17531500 DOI: 10.1016/J.Jasms.2007.04.011  0.431
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  0.77
2007 Zhang Q, Qian WJ, Knyushko TV, Clauss TR, Purvine SO, Moore RJ, Sacksteder CA, Chin MH, Smith DJ, Camp DG, Bigelow DJ, Smith RD. A method for selective enrichment and analysis of nitrotyrosine-containing peptides in complex proteome samples. Journal of Proteome Research. 6: 2257-68. PMID 17497906 DOI: 10.1021/Pr0606934  0.4
2007 Chan EY, Qian WJ, Diamond DL, Liu T, Gritsenko MA, Monroe ME, Camp DG, Smith RD, Katze MG. Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production. Journal of Virology. 81: 7571-83. PMID 17494070 DOI: 10.1128/Jvi.00288-07  0.314
2007 Zhang Q, Tang N, Brock JW, Mottaz HM, Ames JM, Baynes JW, Smith RD, Metz TO. Enrichment and analysis of nonenzymatically glycated peptides: boronate affinity chromatography coupled with electron-transfer dissociation mass spectrometry. Journal of Proteome Research. 6: 2323-30. PMID 17488106 DOI: 10.1021/Pr070112Q  0.713
2007 Liu T, Qian WJ, Camp DG, Smith RD. The use of a quantitative cysteinyl-peptide enrichment technology for high-throughput quantitative proteomics Methods in Molecular Biology. 359: 107-124. PMID 17484113 DOI: 10.1007/978-1-59745-255-7_7  0.429
2007 Kelly RT, Page JS, Tang K, Smith RD. Array of chemically etched fused-silica emitters for improving the sensitivity and quantitation of electrospray ionization mass spectrometry. Analytical Chemistry. 79: 4192-8. PMID 17472340 DOI: 10.1021/Ac062417E  0.419
2007 Belov ME, Buschbach MA, Prior DC, Tang K, Smith RD. Multiplexed ion mobility spectrometry-orthogonal time-of-flight mass spectrometry. Analytical Chemistry. 79: 2451-62. PMID 17305309 DOI: 10.1021/Ac0617316  0.468
2007 Shvartsburg AA, Mashkevich SV, Baker ES, Smith RD. Optimization of algorithms for ion mobility calculations. The Journal of Physical Chemistry. A. 111: 2002-10. PMID 17300182 DOI: 10.1021/Jp066953M  0.593
2007 Shvartsburg AA, Li F, Tang K, Smith RD. Distortion of ion structures by field asymmetric waveform ion mobility spectrometry. Analytical Chemistry. 79: 1523-8. PMID 17297950 DOI: 10.1021/Ac061306C  0.409
2007 Ding SJ, Qian WJ, Smith RD. Quantitative proteomic approaches for studying phosphotyrosine signaling. Expert Review of Proteomics. 4: 13-23. PMID 17288512 DOI: 10.1586/14789450.4.1.13  0.369
2007 Zhang Q, Frolov A, Tang N, Hoffmann R, van de Goor T, Metz TO, Smith RD. Application of electron transfer dissociation mass spectrometry in analyses of non-enzymatically glycated peptides. Rapid Communications in Mass Spectrometry : Rcm. 21: 661-6. PMID 17279487 DOI: 10.1002/Rcm.2884  0.62
2007 Whiteaker JR, Zhang H, Eng JK, Fang R, Piening BD, Feng LC, Lorentzen TD, Schoenherr RM, Keane JF, Holzman T, Fitzgibbon M, Lin C, Zhang H, Cooke K, Liu T, ... ... Smith RD, et al. Head-to-head comparison of serum fractionation techniques. Journal of Proteome Research. 6: 828-36. PMID 17269739 DOI: 10.1021/Pr0604920  0.341
2007 Sharma S, Simpson DC, Tolić N, Jaitly N, Mayampurath AM, Smith RD, Pasa-Tolić L. Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry. Journal of Proteome Research. 6: 602-10. PMID 17269717 DOI: 10.1021/Pr060354A  0.415
2007 Petyuk VA, Qian WJ, Chin MH, Wang H, Livesay EA, Monroe ME, Adkins JN, Jaitly N, Anderson DJ, Camp DG, Smith DJ, Smith RD. Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry. Genome Research. 17: 328-36. PMID 17255552 DOI: 10.1101/Gr.5799207  0.37
2007 Manes NP, Gustin JK, Rue J, Mottaz HM, Purvine SO, Norbeck AD, Monroe ME, Zimmer JS, Metz TO, Adkins JN, Smith RD, Heffron F. Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics. Molecular & Cellular Proteomics : McP. 6: 717-27. PMID 17228056 DOI: 10.1074/Mcp.M600282-Mcp200  0.601
2007 Luo Q, Page JS, Tang K, Smith RD. MicroSPE-nanoLC-ESI-MS/MS using 10-microm-i.d. silica-based monolithic columns for proteomics. Analytical Chemistry. 79: 540-5. PMID 17222018 DOI: 10.1021/Ac061603H  0.413
2007 Shvartsburg AA, Bryskiewicz T, Purves RW, Tang K, Guevremont R, Smith RD. Field asymmetric waveform ion mobility spectrometry studies of proteins: Dipole alignment in ion mobility spectrometry? The Journal of Physical Chemistry. B. 110: 21966-80. PMID 17064166 DOI: 10.1021/jp062573p  0.313
2007 Shvartsburg AA, Tang K, Smith RD. FAIMS operation for realistic gas flow profile and asymmetric waveforms including electronic noise and ripple. Journal of the American Society For Mass Spectrometry. 16: 1447-1455. PMID 16006140 DOI: 10.1016/J.Jasms.2005.04.003  0.312
2007 Page JS, Tang K, Smith RD. An electrodynamic ion funnel interface for greater sensitivity and higher throughput with linear ion trap mass spectrometers International Journal of Mass Spectrometry. 265: 244-250. DOI: 10.1016/J.Ijms.2007.02.032  0.426
2006 Tolmachev AV, Monroe ME, Jaitly N, Petyuk VA, Adkins JN, Smith RD. Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration. Analytical Chemistry. 78: 8374-85. PMID 17165830 DOI: 10.1021/Ac0606251  0.403
2006 Metz TO, Jacobs JM, Gritsenko MA, Fontès G, Qian WJ, Camp DG, Poitout V, Smith RD. Characterization of the human pancreatic islet proteome by two-dimensional LC/MS/MS. Journal of Proteome Research. 5: 3345-54. PMID 17137336 DOI: 10.1021/Pr060322N  0.608
2006 Kelly RT, Page JS, Luo Q, Moore RJ, Orton DJ, Tang K, Smith RD. Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry. Analytical Chemistry. 78: 7796-801. PMID 17105173 DOI: 10.1021/Ac061133R  0.381
2006 Hixson KK, Adkins JN, Baker SE, Moore RJ, Chromy BA, Smith RD, McCutchen-Maloney SL, Lipton MS. Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. Journal of Proteome Research. 5: 3008-17. PMID 17081052 DOI: 10.1021/Pr060179Y  0.33
2006 Valentine SJ, Plasencia MD, Liu X, Krishnan M, Naylor S, Udseth HR, Smith RD, Clemmer DE. Toward plasma proteome profiling with ion mobility-mass spectrometry. Journal of Proteome Research. 5: 2977-84. PMID 17081049 DOI: 10.1021/Pr060232I  0.463
2006 Jaitly N, Monroe ME, Petyuk VA, Clauss TR, Adkins JN, Smith RD. Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Analytical Chemistry. 78: 7397-409. PMID 17073405 DOI: 10.1021/Ac052197P  0.405
2006 Zhang W, Culley DE, Gritsenko MA, Moore RJ, Nie L, Scholten JC, Petritis K, Strittmatter EF, Camp DG, Smith RD, Brockman FJ. LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris. Biochemical and Biophysical Research Communications. 349: 1412-9. PMID 16982031 DOI: 10.1016/J.Bbrc.2006.09.019  0.426
2006 Lipton MS, Romine MF, Monroe ME, Elias DA, Pasa-Tolic L, Anderson GA, Anderson DJ, Fredrickson J, Hixson KK, Masselon C, Mottaz H, Tolic N, Smith RD. AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis. Methods of Biochemical Analysis. 49: 113-34. PMID 16929677 DOI: 10.1002/0471973165.Ch9  0.336
2006 Smith RD. Future directions for electrospray ionization for biological analysis using mass spectrometry Biotechniques. 41: 147-148. PMID 16925015 DOI: 10.2144/000112217  0.446
2006 Norbeck AD, Callister SJ, Monroe ME, Jaitly N, Elias DA, Lipton MS, Smith RD. Proteomic approaches to bacterial differentiation. Journal of Microbiological Methods. 67: 473-86. PMID 16919344 DOI: 10.1016/J.Mimet.2006.04.024  0.359
2006 Zhang H, Loriaux P, Eng J, Campbell D, Keller A, Moss P, Bonneau R, Zhang N, Zhou Y, Wollscheid B, Cooke K, Yi EC, Lee H, Peskind ER, Zhang J, ... Smith RD, et al. UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biology. 7: R73. PMID 16901351 DOI: 10.1186/Gb-2006-7-8-R73  0.593
2006 Shi L, Adkins JN, Coleman JR, Schepmoes AA, Dohnkova A, Mottaz HM, Norbeck AD, Purvine SO, Manes NP, Smallwood HS, Wang H, Forbes J, Gros P, Uzzau S, Rodland KD, ... ... Smith RD, et al. Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages. The Journal of Biological Chemistry. 281: 29131-40. PMID 16893888 DOI: 10.1074/Jbc.M604640200  0.317
2006 Callister SJ, Dominguez MA, Nicora CD, Zeng X, Tavano CL, Kaplan S, Donohue TJ, Smith RD, Lipton MS. Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photosynthetic cell cultures. Journal of Proteome Research. 5: 1940-7. PMID 16889416 DOI: 10.1021/Pr060050O  0.355
2006 Qian WJ, Jacobs JM, Liu T, Camp DG, Smith RD. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Molecular & Cellular Proteomics : McP. 5: 1727-44. PMID 16887931 DOI: 10.1074/Mcp.M600162-Mcp200  0.406
2006 Smith RD, Tang K, Shen Y. Ultra-sensitive and quantitative characterization of proteomes. Molecular Biosystems. 2: 221-30. PMID 16880940 DOI: 10.1039/B601468B  0.377
2006 Liu T, Qian WJ, Mottaz HM, Gritsenko MA, Norbeck AD, Moore RJ, Purvine SO, Camp DG, Smith RD. Evaluation of multiprotein immunoaffnity subtraction for plasma proteomics and candidate biomaker discovery using mass spectrometry Molecular and Cellular Proteomics. 5: 2167-2174. PMID 16854842 DOI: 10.1074/Mcp.T600039-Mcp200  0.356
2006 Petritis K, Kangas LJ, Yan B, Monroe ME, Strittmatter EF, Qian WJ, Adkins JN, Moore RJ, Xu Y, Lipton MS, Camp DG, Smith RD. Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Analytical Chemistry. 78: 5026-39. PMID 16841926 DOI: 10.1021/Ac060143P  0.314
2006 Ibrahim Y, Tang K, Tolmachev AV, Shvartsburg AA, Smith RD. Improving mass spectrometer sensitivity using a high-pressure electrodynamic ion funnel interface. Journal of the American Society For Mass Spectrometry. 17: 1299-305. PMID 16839773 DOI: 10.1016/J.Jasms.2006.06.005  0.367
2006 Callister SJ, Nicora CD, Zeng X, Roh JH, Dominguez MA, Tavano CL, Monroe ME, Kaplan S, Donohue TJ, Smith RD, Lipton MS. Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes. Journal of Microbiological Methods. 67: 424-36. PMID 16828186 DOI: 10.1016/J.Mimet.2006.04.021  0.361
2006 Zhang W, Gritsenko MA, Moore RJ, Culley DE, Nie L, Petritis K, Strittmatter EF, Camp DG, Smith RD, Brockman FJ. A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry. Proteomics. 6: 4286-99. PMID 16819729 DOI: 10.1002/Pmic.200500930  0.381
2006 Sacksteder CA, Qian WJ, Knyushko TV, Wang H, Chin MH, Lacan G, Melega WP, Camp DG, Smith RD, Smith DJ, Squier TC, Bigelow DJ. Endogenously nitrated proteins in mouse brain: links to neurodegenerative disease. Biochemistry. 45: 8009-22. PMID 16800626 DOI: 10.1021/Bi060474W  0.334
2006 Ding YH, Hixson KK, Giometti CS, Stanley A, Esteve-Núñez A, Khare T, Tollaksen SL, Zhu W, Adkins JN, Lipton MS, Smith RD, Mester T, Lovley DR. The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions. Biochimica Et Biophysica Acta. 1764: 1198-206. PMID 16797259 DOI: 10.1016/J.Bbapap.2006.04.017  0.318
2006 Koeniger SL, Merenbloom SI, Valentine SJ, Jarrold MF, Udseth HR, Smith RD, Clemmer DE. An IMS-IMS analogue of MS-MS. Analytical Chemistry. 78: 4161-74. PMID 16771547 DOI: 10.1021/Ac051060W  0.429
2006 Shvartsburg AA, Li F, Tang K, Smith RD. High-resolution field asymmetric waveform ion mobility spectrometry using new planar geometry analyzers. Analytical Chemistry. 78: 3706-14. PMID 16737227 DOI: 10.1021/Ac052020V  0.427
2006 Simpson DC, Ahn S, Pasa-Tolic L, Bogdanov B, Mottaz HM, Vilkov AN, Anderson GA, Lipton MS, Smith RD. Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling. Electrophoresis. 27: 2722-33. PMID 16732621 DOI: 10.1002/Elps.200600037  0.439
2006 Shvartsburg AA, Li F, Tang K, Smith RD. Characterizing the structures and folding of free proteins using 2-D gas-phase separations: observation of multiple unfolded conformers. Analytical Chemistry. 78: 3304-15. PMID 16689531 DOI: 10.1021/Ac060283Z  0.396
2006 Liu T, Qian WJ, Gritsenko MA, Xiao W, Moldawer LL, Kaushal A, Monroe ME, Varnum SM, Moore RJ, Purvine SO, Maier RV, Davis RW, Tompkins RG, Camp DG, Smith RD, et al. High dynamic range characterization of the trauma patient plasma proteome. Molecular & Cellular Proteomics : McP. 5: 1899-913. PMID 16684767 DOI: 10.1074/Mcp.M600068-Mcp200  0.372
2006 Adkins JN, Mottaz HM, Norbeck AD, Gustin JK, Rue J, Clauss TR, Purvine SO, Rodland KD, Heffron F, Smith RD. Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions. Molecular & Cellular Proteomics : McP. 5: 1450-61. PMID 16684765 DOI: 10.1074/Mcp.M600139-Mcp200  0.304
2006 Luo Q, Tang K, Yang F, Elias A, Shen Y, Moore RJ, Zhao R, Hixson KK, Rossie SS, Smith RD. More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry. Journal of Proteome Research. 5: 1091-7. PMID 16674098 DOI: 10.1021/Pr050424Y  0.437
2006 Patwardhan AJ, Strittmatter EF, Camp DG, Smith RD, Pallavicini MG. Quantitative proteome analysis of breast cancer cell lines using 18O-labeling and an accurate mass and time tag strategy. Proteomics. 6: 2903-15. PMID 16596714 DOI: 10.1002/Pmic.200500582  0.347
2006 Page JS, Tolmachev AV, Tang K, Smith RD. Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel. Journal of the American Society For Mass Spectrometry. 17: 586-92. PMID 16503158 DOI: 10.1016/J.Jasms.2005.12.013  0.32
2006 El-Shafey A, Tolic N, Young MM, Sale K, Smith RD, Kery V. "Zero-length" cross-linking in solid state as an approach for analysis of protein-protein interactions. Protein Science : a Publication of the Protein Society. 15: 429-40. PMID 16501223 DOI: 10.1110/Ps.051685706  0.334
2006 Shvartsburg AA, Mashkevich SV, Smith RD. Feasibility of higher-order differential ion mobility separations using new asymmetric waveforms. Journal of Physical Chemistry A. 110: 2663-2673. PMID 16494377 DOI: 10.1021/Jp055349T  0.363
2006 Kiebel GR, Auberry KJ, Jaitly N, Clark DA, Monroe ME, Peterson ES, Toli? N, Anderson GA, Smith RD. PRISM: a data management system for high-throughput proteomics. Proteomics. 6: 1783-90. PMID 16470653 DOI: 10.1002/Pmic.200500500  0.309
2006 Wang H, Qian WJ, Chin MH, Petyuk VA, Barry RC, Liu T, Gritsenko MA, Mottaz HM, Moore RJ, Camp Ii DG, Khan AH, Smith DJ, Smith RD. Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment. Journal of Proteome Research. 5: 361-9. PMID 16457602 DOI: 10.1021/Pr0503681  0.385
2006 Callister SJ, Barry RC, Adkins JN, Johnson ET, Qian WJ, Webb-Robertson BJ, Smith RD, Lipton MS. Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. Journal of Proteome Research. 5: 277-86. PMID 16457593 DOI: 10.1021/Pr050300L  0.402
2006 Zimmer JS, Monroe ME, Qian WJ, Smith RD. Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrometry Reviews. 25: 450-82. PMID 16429408 DOI: 10.1002/Mas.20071  0.394
2006 Elias DA, Monroe ME, Smith RD, Fredrickson JK, Lipton MS. Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1. Journal of Microbiological Methods. 66: 223-33. PMID 16417935 DOI: 10.1016/J.Mimet.2005.11.009  0.302
2006 Fang R, Elias DA, Monroe ME, Shen Y, McIntosh M, Wang P, Goddard CD, Callister SJ, Moore RJ, Gorby YA, Adkins JN, Fredrickson JK, Lipton MS, Smith RD. Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach. Molecular & Cellular Proteomics : McP. 5: 714-25. PMID 16401633 DOI: 10.1074/Mcp.M500301-Mcp200  0.422
2006 Shen Y, Smith RD. Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics. Expert Review of Proteomics. 2: 431-47. PMID 16000088 DOI: 10.1586/14789450.2.3.431  0.438
2006 Shvartsburg AA, Bryskiewicz T, Purves RW, Tang K, Guevremont R, Smith RD. Field asymmetric waveform ion mobility spectrometry studies of proteins: Dipole alignment in ion mobility spectrometry? Journal of Physical Chemistry B. 110: 21966-21980. DOI: 10.1021/Jp062573P  0.384
2005 Wang H, Qian WJ, Mottaz HM, Clauss TR, Anderson DJ, Moore RJ, Camp DG, Khan AH, Sforza DM, Pallavicini M, Smith DJ, Smith RD. Development and evaluation of a micro- and nanoscale proteomic sample preparation method. Journal of Proteome Research. 4: 2397-403. PMID 16335993 DOI: 10.1021/Pr050160F  0.334
2005 Liu T, Qian WJ, Gritsenko MA, Camp DG, Monroe ME, Moore RJ, Smith RD. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. Journal of Proteome Research. 4: 2070-80. PMID 16335952 DOI: 10.1021/Pr0502065  0.41
2005 Patwardhan AJ, Strittmatter EF, Camp DG, Smith RD, Pallavicini MG. Comparison of normal and breast cancer cell lines using proteome, genome, and interactome data. Journal of Proteome Research. 4: 1952-60. PMID 16335939 DOI: 10.1021/Pr0501315  0.378
2005 Shen Y, Strittmatter EF, Zhang R, Metz TO, Moore RJ, Li F, Udseth HR, Smith RD, Unger KK, Kumar D, Lubda D. Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurements. Analytical Chemistry. 77: 7763-73. PMID 16316187 DOI: 10.1021/Ac051257O  0.648
2005 Shen Y, Smith RD, Unger KK, Kumar D, Lubda D. Ultrahigh-throughput proteomics using fast RPLC separations with ESI-MS/MS Analytical Chemistry. 77: 6692-6701. PMID 16223258 DOI: 10.1021/Ac050876U  0.453
2005 Tang K, Li F, Shvartsburg AA, Strittmatter EF, Smith RD. Two-dimensional gas-phase separations coupled to mass spectrometry for analysis of complex mixtures. Analytical Chemistry. 77: 6381-8. PMID 16194103 DOI: 10.1021/Ac050871X  0.452
2005 Huang Y, Triscari JM, Tseng GC, Pasa-Tolic L, Lipton MS, Smith RD, Wysocki VH. Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Analytical Chemistry. 77: 5800-13. PMID 16159109 DOI: 10.1021/Ac0480949  0.339
2005 Shen Y, Kim J, Strittmatter EF, Jacobs JM, Camp DG, Fang R, Tolié N, Moore RJ, Smith RD. Characterization of the human blood plasma proteome. Proteomics. 5: 4034-45. PMID 16152657 DOI: 10.1002/Pmic.200401246  0.391
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