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Acknowledgments
All publications that result from utilization of the Resource must acknowledge NCRR grant support. Please include the following acknowledgment statement:
Portions of this research were supported by the NIH National Center for Research Resources (RR18522), and the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory). Pacific Northwest National Laboratory is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RLO-1830.
DAnTE: a statistical tool for quantitative analysis of -omics data. AD Polpitiya, WJ Qian, N Jaitly, VA Petyuk, JN Adkins, DG Camp II, GA Anderson RD Smith. Bioinformatics, in press (2008).
MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC–MS(/MS) features. ME Monroe, JL Shaw, DS Daly, JN Adkins RD Smith. Comput. Biol. Chem., in press (2008).
DeconMSn: A software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. AM Mayampurath, N Jaitly, SO Purvine, ME Monroe, KJ Auberry, JN Adkins RD Smith. Bioinformatics, 24 (7), 1021-1023 (2008).
Abstract on PubMed
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. ME Monroe, N Tolic, N Jaitly, JL Shaw, JN Adkins RD Smith. Bioinformatics, 23 (15), 2021-2023 (2007).
Abstract on PubMed
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. VA Petyuk, N Jaitly, RJ Moore, J Ding, TO Metz, K Tang, ME Monroe, AV Tolmachev, JN Adkins, ME Belov, AR Dabney, WJ Qian, DG Camp, 2nd RD Smith. Anal. Chem., 80 (3), 693-706 (2008).
Abstract on PubMed
Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags. Y Shen, N Tolic, KK Hixson, SO Purvine, L Pasa-Tolic, WJ Qian, JN Adkins, RJ Moore RD Smith. Anal. Chem., 80 (6), 1871-1882 (2008).
Abstract on PubMed
Capillary-Based Multi Nanoelectrospray Emitters: Improvements in Ion Transmission Efficiency and Implementation with Capillary Reversed-Phase LC-ESI-MS. RT Kelly, JS Page, R Zhao, W Qian, HM Mottaz, K Tang and RD Smith. Anal. Chem., 80 (1), 143-149 (2008).
Abstract on PubMed
Fully Automated Four-Column Capillary LC-MS System for Maximizing Throughput in Proteomic Analyses. EA Livesay, K Tang, BK Taylor, MA Buschbach, DF Hopkins, BL Lamarch, R Zhao, Y Shen, D Orton, RJ Moore, RT Kelly, HR Udseth and RD Smith. Anal. Chem., 80 (1), 294-302 (2008).
Abstract on PubMed
Mitochondrial Dysfunction, Oxidative Stress and Apoptosis Revealed by Proteomic and Transcriptomic Analyses of the Striate in Two Mouse Models of Parkinson’s Disease. MH Chin, W Qian, H Wang, VA Petyuk, JS Bloom, DM Sforza, G Lacan, D Liu, AH Khan, RM Cantor, DJ Bigelow, WP Melega, DG Camp II, RD Smith and DJ Smith. J Proteome Res., 7, 666-677 (2008).
Abstract on PubMed
Spatial Mapping of the Neurite and Soma Proteomes Reveals a Functional Cdc42/Rac Regulatory Network. OC Pertz, Y Wang, F Yang, W Wang, J Gay, MA Gritsenko, TRW Clauss, DJ Anderson, T Liu, KJ Auberry, DC Camp II, RD Smith and RL Klemke. PNAS, 105 (6), 1931-1936 (2008).
Abstract on PubMed
Phosphopeptide elution times in reversed-phase liquid chromatography. J Kim, K Petritis, Y Shen, DG Camp II, RJ Moore and RD Smith. J. Chromatog. A., 1172, 9-18 (2007).
Abstract on PubMed
Targeted Tandem Mass Spectrometry for High-Throughput Comparative Proteomics Employing NanoLC-FTICR MS with External Ion Dissociation. H Kang, L Paša-Tolic, and RD Smith. JASMS, 18, 1332-1343 (2007).
Abstract on PubMed
Ionization and transmission efficiency in an electrospray ionization-mass spectrometry interface. JS Page, RT Kelly, K Tang and RD Smith. JASMS, 18, 1582-1590 (2007).
Abstract on PubMed
Ion Mobility Spectrometry – Mass Spectrometry Performance Using Electrodynamic Ion Funnels and Elevated Drift Gas Pressures. E Baker, BH Clowers, F Li, K Tang, AV Tolmachev, DC Prior, ME Belov and RD Smith. JASMS, 18 (7), 1176-1187 (2007).
Abstract on PubMed
An electrodynamic ion funnel interface for greater sensitivity and higher throughput with linear ion trap mass spectrometers. JS Page, K Tang and RD Smith. IJMS, 265, 244-250 (2007).
Electrospray Characteristic Curves: In Pursuit of Improved Performance in the Nanoflow Regime. I Marginean, RT Kelly, JS Page, K Tang and RD Smith. Anal. Chem., 79, 8030-8036 (2007).
Abstract on PubMed
Array of Chemically Etched Fused-Silica Emitters for Improving the Sensitivity and Quantitation of Electrospray Ionization Mass Spectrometry. RT Kelly, JS Page, K Tang, and RD Smith. Anal. Chem., 79, 4192-4198 (2007).
Abstract on PubMed
Scaling of the Resolving Power and Sensitivity for Planar FAIMS and Mobility-Based Discrimination in Flow- and Field-Driven Analyzer. AA Shvartsburg and RD Smith. JASMS, 18 (9), 1672-1681 (2007).
Abstract on PubMed
Proteomic Profiling of Human Liver Biopsies: Hepatitis C Virus-Induced Fibrosis and Mitochondial Dysfunction. DL Diamond, JM Jacobs, B Paeper, SC Proll, MA Gritsenko, RL Carithers Jr., AM Larson, DG Camp II, RD Smith and MG Katze. Hepatology, 46, 649-657 (2007).
Abstract on PubMed
Identification of a Denitrase Activity in Activated Macrophages Using High-Field FTICR Mass spectrometry. HS Smallwood, NM Lourette, CB Boschek, DJ Bigelow, L Pasa-Tolic, and TC Squier. Biochemistry, 46, 10498-10505 (2007).
Abstract on PubMed
Identification of a Novel Mitotic Phosphorylation Motif Associated with Protein Localization to the Mitotic Apparatus. F Yang, DG Camp, M Gritsenko, Q Luo, R Kelly, TRW Clauss, WR Brinkley, RD Smith, and DL Stenoien. J Cell Sci., 120, 4060-4070 (2007).
Abstract on PubMed
The Mammary Epithelial Cell Secretome and Its Regulation by Signal Transduction Pathways. JM Jacobs, KM Waters, LE Kathmann, DG Camp II, HS Wiley, RD Smith and BD Thrall. J Proteome Res., Electronic (2007).
Abstract on PubMed
Profiling Signaling Polarity in Chemotactic Cells. Y Wang, SJ Ding, W Wang, JM Jacobs, WJ Qian, RJ Moore, F Yang, DG Camp II, RD Smith and RL Klemke. Proc Natl Acad Sci USA, 104 (20), 8328-8333 (2007).
Abstract on PubMed
Applying a Targeted Label-free Approach using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition. F Yang, N Jaitly, H Jayachandran, Q Luo, M Gristenko, ME Monroe, R Zhang, DJ Anderson, SO Purvine, RJ Moore, HM Mottaz, MS Lipton, DG Camp II, HR Udseth, RD Smith and S Rossie. J Proteomic Res., 6 (11), 4489-4497 (2007).
Abstract on PubMed
A Genome-Scale Map of Expression for a Mouse Brain Section Obtained using Voxelation. MH Chin, AB Geng, AH Khan, WJ Qian, VA Petyuk, J Boline, S Levy, AW Toga, RD Smith, RM Leahy, and DJ Smith. Physiol Genomics, 30 (3) 313-321 (2007).
Abstract on PubMed
Whole Proteome Analysis of Post-Translational Modifications: Applications of Mass-Spectrometry for Proteogenomic Annotation. N Gupta, S Tanner, N Jaitly, JN Adkins, MS Lipton, R Edwards, MF Romine, A Osterman, V Bafna, RD Smith and PA Pevzner. Genome Research, 17 (9), 1362-1377 (2007).
Abstract on PubMed
Methods for Pseudopodia Purification and Proteomic Analysis. Y Wang, SJ Ding, W Wang, F Yang, JM Jacobs, DG Camp II, RD Smith and RL Klemke. Sci STKE, 2007 (400), pl4 (2007).
Abstract on PubMed
Quantitative Analysis of Human Immunodeficiency Virus Type 1-Infected CD4+ Cell Proteome: Dysregulated Cell Cycle Progression and Nuclear Transport Coincide with Robust Virus Production. EY Chan, WJ Qian, DL Diamond, T Liu, MA Gritsenko, ME Monroe, DG Camp II, RD Smith and MG Katze. Virol., 81 (14), 7571-7583 (2007).
Abstract on PubMed
Accurate Mass Measurements in Proteomics. T Liu, ME Belov, N Jaitly, W-J Qian and and RD Smith. Chemical Reviews, 107 (8), 3621-3653 (2007).
Abstract on PubMed
A genome-scale map of expression for a mouse brain section obtained using voxelation.MH Chin, AB Geng, AH Khan, WJ Qian, VA Petyuk, J Boline, S Levy, AW Toga, RD Smith, RM Leahy, DJ Smith. Physiological Genomics, 30 (3), 313-321 (2007).
Abstract on PubMed
Application of electron transfer dissociation mass spectrometry in analyses of non-enzymatically glycated peptides. Q Zhang, A Frolov, N Tang, R Hoffmann, T van de Goor, TO Metz, and RD Smith. Rapid Commun. Mass Spectrom., 21 (5), 661-666 (2007).
Abstract on PubMed
Distortion of ion structures by field asymmetric waveform ion mobility spectrometry. AA Shvartsburg, F Li, K Tang, and RD Smith. Anal. Chem., 79 (4), 1523-1528 (2007).
Abstract on PubMed
MicroSPE-nanoLC-ESI-MS/MS using 10-microm-i.d. silica-based monolithic columns for proteomics. Q Luo, JS Page, K Tang, and RD Smith. Anal. Chem., 79 (2), 540-545 (2007).
Abstract on PubMed
Multiplexed ion mobility spectrometry - orthogonal time-of-flight mass spectrometry. ME Belov, MA Buschbach, DC Prior, K Tang, and RD Smith. Anal. Chem., 79 (6), 2451-2462 (2007).
Abstract on PubMed
NanoLC-FT-ICR MS improves proteome coverage attainable for ~3000 laser-microdissected breast carcinoma cells. A Umar, TM Luider, JA Foekens, and L Pasa-Tolic. Proteomics, 7, 323-329 (2007).
Abstract on PubMed
Optimization of algorithms for ion mobility calculations. AA Shvartsburg, SV Mashkevich, EM Baker, and RD Smith. J. Phys. Chem. A, 111 (10), 2002-2010 (2007).
Abstract on PubMed
Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry. S Sharma, DC Simpson, N Tolic, N Jaitly, AM Mayampurath, RD Smith, and L Pasa-Tolic. J. Proteome. Res., 6 (2), 602-610 (2007).
Abstract on PubMed
Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry. VA Petyuk, WJ Qian, MH Chin, H Wang, EA Livesay, ME Monroe, JN Adkins, N Jaitly, DJ Anderson, DG Camp, DJ Smith, and RD Smith. Genome Res., 17 (3), 328-336 (2007).
Abstract on PubMed (free full text)
Quantitative proteomic approaches for studying phosphotyrosine signaling. SJ Ding, WJ Qian, RD Smith. Expert. Rev. Proteomics, 4 (1), 13-23 (2007).
Abstract on PubMed
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. ME Monroe, N Tolić, N Jaitly, JL Shaw, JN Adkins, RD Smith. Bioinformatics, 23 (15), 2021-2023 (2007).
Abstract on PubMed
High Dynamic Range Characterization of the Trauma Patient Plasma Proteome and the Inflammation and the Host Response to Injury Large Scale Collaborative Research Program.T Liu, W-J Qian, MA Gritsenko, W Xiao, LL Moldawer, A Kaushal, RJ Moore, SO Purvine, RV Maier, RW Davis, RG Tompkins, DG Camp II, and RD Smith. Mol. Cell. Proteomics, 5 (10), 1899-1913 (2006).
Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. WJ Qian, JM Jacobs, T Liu, DG Camp, and RD Smith. Mol. Cell. Proteomics, 5 (10), 1727-1744 (2006).
Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS. TO Metz, JM Jacobs, MA Gritsenko, G. Fontes, W.-J. Qian, D. Camp II, V. Poitout, RD Smith. J. Proteome Res., 5 (12), 3345-3354 (2006). Download the supplemental data corresponding to this article - 1 Excel file (5.2 MB) (registration required).
Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics. T Baas, CR Baskin, DL Diamond, A García-Sastre, H Bielefeldt-Ohmann, TM Tumpey, MJ Thomas, VS Carter, TH Teal, N Van Hoeven, S Proll, JM Jacobs, ZR Caldwell, MA Gritsenko, RR Hukkanen, DG Camp II, RD Smith, MG Katze. Journal of Virology, 80 (21) (2006). Download the supplemental data corresponding to this article - 1 Excel file (845 KB) (registration required).
Advances in Proteomics Data Analysis and Display
Using an Accurate Mass and Time Tag Approach. JS Zimmer, ME
Monroe, W Qian, and RD Smith. Mass
Spectrometry Reviews, 25 (3), 450-482 (2006).
Abstract on PubMed
Feasibility of Higher-Order Differential Ion Mobility Separations Using New Asymmetric Waveforms. Shvartsburg AA, SV Mashkevich, and RD Smith. Journal of Physical Chemistry A, 110 (8), 2663-2673 (2006).
Quantitative Proteome Analysis of Breast Cancer Cell Lines using 18O-Labeling and an Accurate Mass and Time Tag Strategy. Patwardhan AJ, EF Strittmatter, DG Camp, II, RD Smith, and M Pallavicini, Proteomics, 6 (9), 2903-2915 (2006). doi:10.1002/pmic200500582
Characterizing the Structures and Folding of Free Proteins Using 2-D Gas-Phase Separations: Observation of Multiple Unfolded Conformers. Shvartsburg AA, F Li, K Tang, and RD Smith, Analytical Chemistry, 78 (10), 3304-3315 (2006).
Characterization of the Mouse Brain Proteome Using
Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment. Wang
HH, W Qian, MH Chin, VA Petyuk, RC Barry, T Liu, MA Gritsenko, HM Mottaz,
RJ Moore, DG Camp, II, AH Khan, D Smith, and RD Smith. Journal
of Proteome Research, 5 (2), 361-369 (2006).
Abstract on PubMed (free in PMC)
Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry. RT Kelly, JS Page, Q Luo, RJ Moore, DJ Orton, K Tang, and RD Smith. Anal. Chem., 78 (22), 7796-7801 (2006).
Data merging for integrated microarray and proteomic analysis. KM Waters, JG Pounds, and BD Thrall. Brief Funct. Genomic Proteomic, 5, 261-272 (2006).
Endogenously nitrated proteins in mouse brain: Links to neurodegenerative disease. CA Sacksteder, WJ Qian, TV Knyushko, H Wang, MH Chin, G Lacan, WP Melega, DG Camp, 2nd, RD Smith, DJ Smith, TC Squier, and DJ Bigelow. Biochem., 45 (26), 8009-8022 (2006).
Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. T Liu, WJ Qian, HM Mottaz, MA Gritsenko, AD Norbeck, RJ Moore, SO Purvine, DG Camp, and RD Smith. Mol. Cell. Proteomics, 5 (11), 2167-2174 (2006).
Field asymmetric waveform ion mobility spectrometry studies of proteins: Dipole alignment in ion mobility spectrometry. AA Shvartsburg, T Bryskiewicz, RW Purves, K Tang, R Guevremont, and RD Smith. J. Phys. Chem. B Condens. Matter Mater. Surf. Interfaces Biophys., 110 (43), 21966-21980 (2006).
Future directions for electrospray ionization for biological analysis using mass spectrometry. RD Smith. Biotechniques, 41 (2), 147-148 (2006).
HepatoProteomics: applying proteomic technologies to the study of liver function and disease. DL Diamond, SC Proll, JM Jacobs, EY Chan, DG Camp, 2nd, RD Smith, and MG Katze. Hepatology, 44 (2), 299-308 (2006).
Increases in calmodulin abundance and stabilization of activated inducible nitric oxide synthase mediate bacterial killing in RAW 264.7 macrophages. HS Smallwood, L Shi, and TC Squier. Biochemistry, 45 (32), 9717-9726 (2006).
Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional
recalibration. AV Tolmachev, ME Monroe, N Jaitly, VA Petyuk, JN Adkins, and RD Smith.
Anal. Chem., 78 (24), 8374-8385 (2006).
Abstract on PubMed
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. SJ Callister, RC Barry, JN Adkins, ET Johnson, WJ Qian, BJ Webb-Robertson, RD Smith, and MS Lipton. J. Proteome Res., 5 (2), 277-286 (2006).
PRISM: A data management system for high-throughput proteomics. GR Kiebel, KJ Auberry,
N Jaitly, DA Clark, ME Monroe, ES Peterson, N Tolic, GA Anderson, and RD Smith. Proteomics, 6 (6), 1783-1790 (2006).
Abstract on PubMed
Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate
mass and time tag data analysis pipeline. N Jaitly, ME Monroe, VA Petyuk, TR Clauss, JN Adkins,
and RD Smith. Anal. Chem., 78 (21), 7397-7409 (2006).
Abstract on PubMed
Toward plasma proteome profiling with ion mobility-mass spectrometry. SJ Valentine, MD Plasencia, X Liu, M Krishnan, S Naylor, HR Udseth, RD Smith, and DE Clemmer. J. Proteome Res., 5 (11), 2977-2984 (2006).
Statistical evaluation of the big bang search algorithm. Jackson KA, M Horoi, I Chaudhuri, T Frauenheim, and AA Shvartsburg. Computational Materials Science, 35 (3), 232-37 (2006).
Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel. Page JS, AV Tolmachev, K Tang, and RD Smith. Journal of the American Society for Mass Spectrometry, 17 (4), 586-592 (2006).
High-Resolution Field Asymmetric Waveform Ion Mobility Spectrometry Using New Planar Geometry Analyzers. Shvartsburg AA, F Li, K Tang, and RD Smith. Analytical Chemistry, 78 (11), 3706-3714 (2006).
More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry. Luo Q, K Tang, F Yang, A Elias, Y Shen, RJ Moore, R Zhao, KK Hixson, SS Rossie, and RD Smith, Journal of Proteome Research, 5 (5), 1091-1097 (2006).
Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling. Simpson DC, S Ahn, L Pasa-Tolic, B Bogdanov, HM Mottaz, AN Vilkov, GA Anderson, MS Lipton, and RD Smith. Electrophoresis, 7 (13), 2722-2733 (2006).
Improved peptide elution time prediction for reversed-phase liquid chromatography-MS
by incorporating peptide sequence information. K Petritis, LJ
Kangas, B Yan, ME Monroe, EF Strittmatter, W Qian, JN Adkins, RJ Moore,
Y Xu, MS Lipton, DG Camp, II, and RD Smith, Analytical
Chemistry, 78 (14), 5026-5039 (2006).
Abstract on PubMed
Making Broad Proteome Protein Measurements in 1-5 min using High-Speed RPLC Separations and High-Accuracy Mass Measurements. Y Shen, EF Strittmatter, R Zhang, TO Metz, RJ Moore, F Li, HR Udseth, RD Smith, KK Unger, D Kumar, and D Lubda, Analytical Chemistry, 77, 7763-7773 (2005).
Ultrahigh-Throughput Proteomics using RPLC-MS/MS. Y Shen and RD Smith, Analytical Chemistry, 77, 6692-6701 (2005).
Two-Dimensional Gas-Phase Separations Coupled to Mass Spectrometry for Analyses of Complex Mixtures. K Tang, F Li, AA Shvartsburg, EF Strittmatter, and RD Smith, Analytical Chemistry, 77, 6381-6388 (2005).
Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns. Y Huang, JM Triscari, GC Tseng, L Pasa-Tolic, MS Lipton, RD Smith, and VH Wysocki, Analytical Chemistry, 77, 5800-5812 (2005).
Preparation of 20-um-i.d. Silica-Based Monolithic Columns and Their Performance for Proteomics Analyses. Q Luo, Y Shen, KK Hixson, R Zhao, F Yang, RJ Moore, HM Mottaz, and RD Smith, Analytical Chemistry, 77, 5028-5035 (2005).
High-Sensitivity Ion Mobility Spectrometry/Mass Spectrometry Using Electrodynamic Ion Funnel Interfaces. K Tang, AA Shvartsburg, H-N Lee, DC Prior, MA Buschbach, F Li, A Tolmachev, GA Anderson, and RD Smith, Analytical Chemistry, 77, 3330-3339 (2005).
Automated 20 Kpsi RPLC-MS and MS/MS with Chromatographic Peak Capacities of 1,000-1,500 for Proteomics and Metabolomics. Y Shen, R Zhang, RJ Moore, J Kim, TO Metz, KK Hixson, R Zhao, EA Livesay, HR Udseth, and RD Smith, Analytical Chemistry, 77, 3090-3100 (2005).
Targeted Comparative Proteomics by Liquid Chromatography - Tandem Fourier Transform Mass Spectrometry. C Masselon, L Pasa-Tolic, N Tolic, GA Anderson, B Bogdanov, AN Vilkov, Y Shen, R Zhao, W Qian, MS Lipton, DG Camp II and RD Smith, Analytical Chemistry, 77, 400-406 (2005).
Combining Capillary Electrophoresis with Mass Spectrometry for Applications in Proteomics. DC Simpson and RD Smith, Electrophoresis, 26, 1291-1303 (2005).
Advanced Nanoscale Separations and Mass Spectrometry for Sensitive High-Throughput Proteomic. Y Shen and RD Smith, Expert Review of Proteomics, 2, 431-447 (2005).
FAIMS Operation for Realistic Gas Flow Profile and Asymmetric Waveforms Including Electronic Noise and Ripple. AA Shvartsburg, K Tang, and RD Smith, Journal of the American Society for Mass Spectrometry, 16, 1447-1455 (2005).
The Utility of Accurate Mass and LC Elution Time Information
in the Analysis of Complex Proteomes. AD Norbeck, ME Monroe,
JN Adkins, and RD Smith, Journal of the American Society for Mass
Spectrometry , 16, 1239-1249 (2005).
Abstract on PubMed
Optimization of the Design and Operation of FAIMS Analyzers. AA Shvartsburg, K Tang and RD Smith, Journal of the American Society for Mass Spectrometry, 16, 2-12 (2005).
Variable Low-Mass Filtering using an Electrodynamic Ion Funnel. JS Page, AV Tolmachev, K Tang, and RD Smith, Journal of Mass Spectrometry, 40, 1215-1222 (2005).
Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method. HH Wang, W Qian, HM Mottaz, T Clauss, DJ Anderson, RJ Moore, DG Camp II, AH Khan, DM Sforza, M Pallavicini, DJ Smith, and RD Smith, Journal of Proteome Research, 4, 2397-2403 (2005).
Comparison of Normal and Breast Cancer Cell Lines using Proteome, Genome, and Interactome Data. AJ Patwardhan, EF Strittmatter, DG Camp II, RD Smith, and M Pallavicini, Journal of Proteome Research, 4, 1952-1960 (2005).
Utilizing Human Blood Plasma for Proteomic Biomarker Discovery. JM Jacobs, JN Adkins, W-J Qian, T Liu, Y Shen, DG Camp II, and RD Smith, Journal of Proteome Research, 4, 1073-1085 (2005).
Proteome Analysis of Liver Cells Expressing a Full-length Hepatitis C Virus (HCV) Replicon and Biopsies of Post-transplanted Liver from HCV-infected Patients. JM Jacobs, DL Diamond, EY Chan, MA Gritsenko, W Qian, M Stastna, T Baas, DG Camp II, RL Carithers, Jr., RD Smith, and MG Katze, Journal of Virology, 79, 7558-7569 (2005). Download the supplemental data corresponding to this article - 1 Excel file (845 KB) (registration required).
Proteomics by FTICR Mass Spectrometry: Top Down and Bottom Up. B Bogdanov and RD Smith, Mass Spectrometry Reviews, 24, 168-200 (2005).
Global Analysis of the Response of Human Mammary Epithelial Cells to Epidermal Growth Factor Stimulation. BD Thrall, LE Kathmann, T Liu, RD Quesenbery, TJ Weber, JM Jacobs, RD Smith, B Gopalan, and HS Wiley, Molecular Biology of the Cell, 15, (supplement), 65 (2005).
Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry. T Liu, W-J. Qian, MA Gritsenko, DG Camp II, ME Monroe, RJ Moore, and RD Smith, Molecular and Cellular Proteomics, 4, 2070-2080 (2005).
Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using 16O/18O Labeling and the Accurate Mass and Time Tag Approach. W-J Qian, ME Monroe, T Liu, JM Jacobs, GA Anderson, Y Shen, RJ Moore, DJ Anderson, R Zhang, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DG Camp II, and RD Smith, Molecular and Cellular Proteomics; 4, 700-709 (2005).
High Throughput Quantitative Analysis of Serum Proteins using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry. H Zhang, EC Yi, X Li, P Mallick, KS Spratt, CD Masselon, DG Camp II, RD Smith, C Kemp, and R Aebersold, Molecular and Cellular Proteomics, 4, 144-155 (2005).
Characterization of the Human Blood Plasma Proteome. Y Shen, J Kim, EF Strittmatter, JM Jacobs, DG Camp II, R Fang, N Tolic, RJ Moore, and RD Smith, Proteomics, 5, 4034-4045 (2005).
A Proteomic Study of HUPO's Plasma Proteome Project Pilot Samples using an Accurate Mass and Time Tag Strategy. JN Adkins, ME Monroe, KJ Auberry, Y Shen, JM Jacobs, DG Camp II, F Vitzthum, KD Rodland, RD Smith, and JG Pounds, Proteomics, 5, 3454-3466 (2005).
High-throughput Proteomics using Fourier Transform Ion Cyclotron Resonance (FTICR) Mass Spectrometry. W-J Qian, DG Camp, and RD Smith, Expert Review of Proteomics, 1, 87-95 (2005).
Proteomic Analysis of Lyme Disease: Global Protein Comparison of Three Strains of Borrelia burgdorferi. JM Jacobs, X Yang, BJ Luft, JJ Dunn, DG Camp II, and RD Smith, Proteomics, 5, 1446-1453. Download the supplemental data corresponding to this article - 1 Excel file (1.7 MB) (registration required).
Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements. JM Jacobs, ME Monroe, W-J Qian, Y Shen, GA Anderson, and RD Smith, International Journal of Mass Spectrometry, 240, 195-212 (2005).
Improved Proteome Coverage by Using High Efficiency Cysteinyl Peptide Enrichment: The Human Mammary Epithelial Cell Proteome. T Liu, W-J Qian, W-NU Chen, JM Jacobs, RJ Moore, DJ Anderson, MA Gritsenko, ME Monroe, BD Thrall, DG Camp and RD Smith, Proteomics, 5, 1263-1273 (2005).
Probability-Based Evaluations of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome. W-J Qian, T Liu, ME Monroe, EF Strittmatter, JM Jacobs, LJ Kangas, K Petritis, DG Camp II and RD Smith, Journal of Proteome Research, 4, 53-62 (2005).
Automatic Gain Control in Mass Spectrometry using a Jet Disrupter Electrode in an Electrodynamic Ion Funnel. JS Page, B Bogdanov, AN Vilkov, DC Prior, MA Buschbach, K Tang, and RD Smith, Journal of the American Society for Mass Spectrometry, 16 (2), 244-253 (2005).
Comparative Proteome Analyses of Human Plasma Following in vivo Lipopolysaccharide Administration Using Multidimensional Separations Coupled with Tandem Mass Spectrometry. W-J Qian, JM Jacobs, DG Camp II, ME Monroe, RJ Moore, MA Gritsenko, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, and RD Smith, Proteomics, 5, 572-584 (2005).
Sites of Proteolytic Processing and Noncovalent Association of the Distal C-terminal Domain of Cav1.1 Channels in Skeletal Muscle. JT Hulme, K Konoki, T. W-C Lin, MA Gritsenko, DG Camp II, DJ Bigelow, WA Catterall, Proceedings of the National Academy of Science, 102, 5274-5279 (2005).
Ultrasensitive and Quantitative Analyses from Combined Separations-Mass Spectrometry for the Characterization of Proteomes. RD Smith, Y Shen, and K Tang, Accounts of Chemical Research, 37, 269-278 (2004).
Understanding and Designing Field Asymmetric Waveform Ion Mobility Spectrometry Separations in Gas Mixtures. AA Shvartsburg, K Tang, and RD Smith, Analytical Chemistry, 76, 7366-7374 (2004).
High-Throughput Comparative Proteome Analysis Using a Quantitative Cysteinyl-peptide Enrichment Technology. T Liu, W-J Qian, EF Strittmatter, DG Camp, GA Anderson, BD Thrall, and RD Smith, Analytical Chemistry , 76, 5345-5353 (2004).
Ultra-High-Efficiency Strong Cation Exchange LC/RPLC/MS/MS for High Dynamic Range Characterization of the Human Plasma Proteome. Y Shen, JM Jacobs, DG Camp, R Fang, RJ Moore, RD Smith, W Xiao, RW Davis, and RG Tompkins, Analytical Chemistry, 76, 1134-1144 (2004).
Proteomic Analyses using an Accurate Mass and Time Tag Strategy. L Pasa-Tolic, C Masselon, RC Barry, Y Shen, and RD Smith, BioTechniques, 37, 621-639 (2004).
Ultrasensitive Proteomics Using High-Efficiency On-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS. Y Shen, N Tolic, C Masselon, L Pasa-Tolic, DG Camp II, KK Hixon, R Zhao, GA Anderson, and RD Smith, Analytical Chemistry, 76, 144-154 (2004).
FTICR Mass Spectrometry for Qualitative and Quantitative Bioanalyses. JS Page, CD Masselon, and RD Smith, Current Opinion in Biotechnology, 15, 3-11 (2004).
A Rational Approach for Discovering and Validating Cancer Markers in Very Small Samples Using Mass Spectrometry and ELISA Microarrays. RC Zangar, SM Varnum, CY Covington and RD Smith, Disease Markers, 20, 135-148 (2004).
Collisional Activation of Ions in RF Ion Traps and Ion Guides: the Effective Ion Temperature Treatment. AV Tolmachev, AN Vilkov, B Bogdanov, L Pasa-Tolic, CD Masselon, and RD Smith, Journal of the American Society for Mass Spectrometry, 15, 1616-1628 (2004).
Modeling the Resolution and Sensitivity of FAIMS Analyses. AA Shvartsburg, Tang K, and RD Smith, Journal of the American Society for Mass Spectrometry, 15, 1487-1498 (2004).
Charge Competition and the Linear Dynamic Range of Detection in Electrospray Ionization Mass Spectrometry. K Tang, JS Page and RD Smith, Journal of the American Society for Mass Spectrometry, 15, 1416-1423 (2004).
Application of Peptide Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry. EF Strittmatter, LJ Kangas, K Petritis, HM Mottaz, GA Anderson, Y Shen, JM Jacobs, DG Camp, and RD Smith, Journal of Proteome Research, 3, 760-769 (2004).
Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome. SM Varnum, DN Streblow, ME Monroe, P Smith, KJ Auberry, L Pasa-Tolic, D Wang, DG Camp II, K Rodland, S Wiley, W Britt, T Shenk, RD Smith, and JA Nelson, Journal of Virology, 78, 10,960-10,966 (2004).
Proteomic Analyses using High Efficiency Separations and Accurate Mass Measurements. JM Jacobs and RD Smith, Separation Methods in Proteomics Chapt. 20, Edited by Smejkal and Lazareu, CRC Taylor and Francis Group, Madison, WI; (2006), 363-385.
A proteomics analysis of human cytomegalovirus particles. DN Streblow, SM Varnum, RD Smith, and JA Nelson, Cytomegaloviruses: molecular biology and immunology, Raeddehase, Caister Academic Press: Hethersett, United Kingdom, (2006), Chapter 5.
The use of quantitative cysteinyl-peptide enrichment technology for high-throughput quantitative proteomics. T Liu, WJ Qian, DG Camp, 2nd, and RD Smith, Quantitative proteomics by mass spectrometry (Methods in molecular biology series), S. Sechi, Humana Press: Totowa, New Jersey, (2006), Chapter 8.
The Use of Accurate Mass and Time Tags based upon High-Throughput Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Global Proteomic Characterization. DG Camp II and RD Smith, "Proteome Analysis: Interpreting the Genome" (Ed. DW Spiecher), Elsevier B.V., Amsterdam, The Netherlands; (2004), Chapter 8, 183-224.
