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1. Unexpected Peaks in Tandem Mass Spectra due to Reaction of Product Ions with Water in Mass
Spectrometer Collision Cells
Pedatsur Neta, Mahnaz Farahani, Yamil Simon, Yuxue Liang, Xiaoyu Yang, Stephen E Stein
While determining the fragmentation pathways of positive ions of drugs, pesticides, metabolites, and
other compounds, using electrospray ionization mass spectrometry, we noticed that certain product
ions react with water in the collision cell. Th ...
2. Creation of Libraries of Recurring Mass Spectra from Large Data Sets assisted by a Dual-Column
William Gary Mallard, Stephen E Stein, Halket M John, Yuri Alexander Mirokhin, Nirina Rabe Andriamaharavo
An analytical methodology has been developed for extracting recurrent unidentified spectra (RUS)
from large GC/MS data sets. Spectra were first extracted from original data files by the Automated
Mass Spectral Deconvolution and Identification Sys ...
3. 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 ...
4. 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 ...
5. 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 ...
6. 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 ...
7. CPTAC Studies 1 and 5: dissecting variability in multi-site LC-MS/MS proteomics through quality
metrics and robust hierarchical multivariate statistics
Stephen E Stein, David M Bunk, Xia Wang, Matthew Chambers, Lorenzo J Vega-Montoto, David L. Tabb
Shotgun proteomics experiments integrate a complex sequence of processes, any of which can introduce variability. Quality metrics computed from LC-MS/MS data have relied upon identifying MS/MS scans, but a new mode for the QuaMeter software produces ...
8. 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 ...
9. 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 ...
10. 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 ...