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Author: Paul Rudnick

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1. Improved Normalization of Systematic Biases Affecting Ion Current Measurements in Label-free Proteomics Data
Published: 2/21/2014
Authors: Paul A Rudnick, Xinjian Yan, Stephen E Stein, Xia Wang, Nell Sedransk
Abstract: Systematic biases, or batch effects, in ,high-throughput‰ biological datasets can be described as obscuring variabilities introduced during experimental design or analytical processing. These biases, if left unresolved, can lead to misinterpreta ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=913822

2. Metabolite Profiling of a NIST Standard Reference Material for Human Plasma (SRM 1950) ‹ GC/MS, LC/MS, NMR and Clinical Laboratory Analyses, Libraries and Web-based resources
Published: 10/22/2013
Authors: Yamil Simon, Mark S Lowenthal, Lisa Ervin Kilpatrick, Maureen L Sampson, Kelly H Telu, Paul A Rudnick, William Gary Mallard, Daniel W Bearden, Tracey Beth Schock Schock, Dmitrii V Tchekhovskoi, Niksa Blonder, Xinjian Yan, Yuxue Liang, Yufang Zheng, William E Wallace III, Pedatsur Neta, Karen W Phinney, Alan T. Remaley, Stephen E Stein
Abstract: Recent progress in metabolomics and the development of increasingly sensitive analytical techniques have renewed interest in global profiling, i.e., semi-quantitative monitoring of all chemical constituents of biological fluids. In this work, we have ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=913835

3. Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics
Published: 10/11/2013
Authors: Stephen E Stein, Paul A Rudnick, Scott J Walmsley, Qian Dong, Alexey I Nesvizhskii, Yuxue Liang
Abstract: Trypsin is an endoprotease commonly used for sample preparation in proteomics experiments. Importantly, protein digestion is dependent on multiple factors, including the trypsin origin and digestion conditions. In-depth characterization of tryp ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=914042

4. Developing qualitative LC-MS methods for characterization of Vaccinium berry Standard Reference Materials
Published: 9/2/2012
Authors: Mark S Lowenthal, Melissa Meaney Phillips, Catherine A Rimmer, Paul A Rudnick, Yamil Simon, Stephen E Stein, Karen W Phinney
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=911317

5. Depletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics
Published: 10/1/2010
Authors: Chengjian Tu, Paul A Rudnick, Misti Y. Martinez, Kristin L. Cheek, Stephen E Stein, Robert J. Slebos, Daniel C. Liebler
Abstract: Immunoaffinity depletion of high abundance plasma proteins is frequently employed to enhance detection of lower abundance proteins in both shotgun and targeted proteomic analyses. Here we present a detailed evaluation of the Agilent Multiple Affinit ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=905138

6. A Multi-site Assessment of Precision and Reproducibility of Multiple Reaction Monitoring-based Measurements: Toward Quantitative Protein Biomarker Verification in Human Plasma
Published: 6/28/2009
Authors: Nathan G. Dodder, Terri Addona, Susan Abbatiello, Birgit Schilling, Steven Skates, D.R. Mani, David M Bunk, Clifford Spiegelman, Lisa Zimmerman, Amy-Joan Ham, Hasmik Keshishian, Steven Hall, Simon Allen, Ronald Blackman, Christoph Borchers, Charles Buck, Helene Cardasis, Michael Cusack, Bradford Gibson, Jason Held, Tara Hiltke, Angela Jackson, Eric Johansen, Christopher Kinsinger, Jing Li, Mehdi Mesri, Thomas Neubert, Richard Niles, Trenton Pulsipher, Henry Rodriguez, Paul A Rudnick, Derek Smith, David Tabb, Tony Tegeler, Henry Variyath, Lorenzo Vega-Montoto, Asa Wahlander, Sofia Waldemarson, Mu Wang, Jeffrey Whitaker, Lei Zhao, N. Leigh Anderson, Susan Fisher, Daniel Liebler, Amanda Paulovich, Fred Regnier, Paul Tempst, Steven Carr
Abstract: Candidate-based biomarker verification relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the biomarker discovery pipeline that bridges unbiased discovery t ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=901703



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