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Author: Stephen Stein
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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. Quantitative bottom-up proteomics depends on digestion conditions
Mark S Lowenthal, Yuxue Liang, Karen W Phinney, Stephen E Stein
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 ...
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
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 ...
4. 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 ...
5. Characterizing Vaccinium berry Standard Reference Materials using NIST Mass Spectral Libraries
Mark S Lowenthal, Nirina Rabe Andriamaharavo, Stephen E Stein, Karen W Phinney
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 ...
6. 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
7. Extension of ThermoML: The IUPAC Standard for Thermodynamic Data Communications (IUPAC Recommendations 2011)
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
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 ...
8. Electron Ionization Mass Spectra of Alkylated Sulfabenzamides
Nino Guram Todua, Kirill V. Tretyakov, Roman S. Borisov, Dmitry I. Zhilyaev, Vladimir G. Zaikin, Stephen E Stein, Anzor I. Mikaia
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 ...
9. Charge States of y Ions in the Collision-Induced Dissociation of Doubly Charged Tryptic Peptide Ions
Pedatsur Neta, Stephen E Stein
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 ...
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
Yamil Simon, Pedatsur Neta, Xiaoyu Yang, Stephen E Stein
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 ...