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1. Loss of H2 and CO from Protonated Aldehydes in Electrospray Ionization Mass Spectrometry
Pedatsur Neta, Yamil Simon, Yuxue Liang, Stephen E Stein
Electrospray ionization mass spectrometry of 3-formylchromones and 3-formylcoumarins shows that
collision-induced dissociation of the protonated ions results in elimination of H¬¬2 as a major
fragmentation route. This loss of H2 yields an unstabl ...
2. Computer-Assisted Quality Control for Building Libraries from Electrospray Ionization Tandem Mass
Xiaoyu Yang, Pedatsur Neta, Stephen E Stein
Electrospray ionization (ESI) tandem mass spectrometry coupled with liquid chromatography is a
routine technique for identifying and quantifying compounds in complex mixtures. The identification
step can be aided by matching acquired tandem mass ...
3. Tandem Mass Spectral Libraries of Peptides in Digests of Individual Proteins: Human Serum Albumin
Qian Dong, Xinjian Yan, Lisa Ervin Kilpatrick, Yuxue Liang, Yuri Alexander Mirokhin, Jeri S Roth, Stephen E Stein
This work presents a method for creating a mass spectral library containing tandem spectra
identifiable peptide ions in the tryptic digestion of a single protein. Human serum albumin (HSA)
was selected for this purpose owing to its ubiquity and h ...
4. 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 ...
5. 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 ...
6. 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 ...
7. 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 ...
8. 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 ...
9. 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
10. 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 ...