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Author: Paul Rudnick
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1. Improved Normalization of Systematic Biases Affecting Ion Current Measurements in Label-free
Paul A Rudnick, Xinjian Yan, Stephen E Stein, Xia Wang, Nell Sedransk
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 ...
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
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
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 ...
3. Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a
significant source of variability in proteomics
Stephen E Stein, Paul A Rudnick, Scott J Walmsley, Qian Dong, Alexey I Nesvizhskii, Yuxue Liang
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 ...
4. Developing qualitative LC-MS methods for characterization of Vaccinium berry Standard Reference Materials
Mark S Lowenthal, Melissa Meaney Phillips, Catherine A Rimmer, Paul A Rudnick, Yamil Simon, Stephen E Stein, Karen W Phinney
5. Depletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics
Chengjian Tu, Paul A Rudnick, Misti Y. Martinez, Kristin L. Cheek, Stephen E Stein, Robert J. Slebos, Daniel C. Liebler
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 ...
6. A Multi-site Assessment of Precision and Reproducibility of Multiple Reaction Monitoring-based Measurements: Toward Quantitative Protein Biomarker Verification in Human Plasma
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
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 ...