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Author: stephen stein
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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. Quantitative bottom-up proteomics depends on digestion conditions
Published: 12/2/2013
Authors: Mark S Lowenthal, Yuxue Liang, Karen W Phinney, Stephen E Stein
Abstract: Accurate quantification is a fundamental requirement in the fields of proteomics and biomarker discovery, and for clinical diagnostic assays. To demonstrate the extent of quantitative variability in measurable peptide concentrations due to differenc ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=914393

3. 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

4. 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

5. Characterizing Vaccinium berry Standard Reference Materials using NIST Mass Spectral Libraries
Published: 1/6/2013
Authors: Mark S Lowenthal, Nirina Rabe Andriamaharavo, Stephen E Stein, Karen W Phinney
Abstract: A gas chromatography-mass spectrometry-based (GC-MS) method was developed for qualitative characterization of metabolites found in Vaccinium-fruit (berry) dietary supplement Standard Reference Materials (SRMs). Definitive identifications are pro ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=912593

6. 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

7. Extension of ThermoML: The IUPAC Standard for Thermodynamic Data Communications (IUPAC Recommendations 2011)
Published: 9/7/2011
Authors: Michael Frenkel, Robert D Chirico, Vladimir Diky, Paul L Brown, John H. Dymond, Robert Nathan Goldberg, Anthony R.H. Goodwin, Heiko Heerklotz, Erich Koenigsberger, John E. Ladbury, Kenneth N. Marsh, David P. Remeta, Stephen E Stein, William A. Wakeham, Peter A Williams
Abstract: ThermoML is an XML-based approach for storage and exchange of experimental, predicted, and critically evaluated thermophysical and thermochemical property data. Extensions to the ThermoML schema for the representation of speciation, complex equilibri ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=908392

8. Electron Ionization Mass Spectra of Alkylated Sulfabenzamides
Published: 3/30/2011
Authors: Nino Guram Todua, Kirill V. Tretyakov, Roman S. Borisov, Dmitry I. Zhilyaev, Vladimir G. Zaikin, Stephen E Stein, Anzor I. Mikaia
Abstract: Mono-, di- and trialkyl derivatives of "sulfabenzamide" (N-4-aminophenylsulfonyl-benzamide) are prepared and their EI mass spectra are examined. It is found that the fragmentation of N- alkylsulfabenzamides (Alkyl = CH3 to n-C5H11) proceeds via a ver ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=907083

9. Charge States of y Ions in the Collision-Induced Dissociation of Doubly Charged Tryptic Peptide Ions
Published: 2/25/2011
Authors: Pedatsur Neta, Stephen E Stein
Abstract: Bonds that break in collision-induced dissociation (CID) are often weakened by a nearby proton, which can, in principle, be carried away by either of the product fragments. Since peptide backbone dissociation is commonly charge-directed, relative int ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=907257

10. Loss of 45 Da from a2 Ions and Preferential Loss of 48 Da from a2 Ions Containing Methionine in Peptide Ion Tandem Mass Spectra
Published: 1/29/2011
Authors: Yamil Simon, Pedatsur Neta, Xiaoyu Yang, Stephen E Stein
Abstract: While analyzing tandem mass spectra of tryptic tripeptides, intense unassigned peaks were observed, which correspond to a neutral loss of 45 Da from a^d2^ ions. From exact mass analysis this loss is ascribed to formamide (or NH^d3^+CO). Elimination o ...
http://www.nist.gov/manuscript-publication-search.cfm?pub_id=906270



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