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Search Publications by: Stephen E. Stein (Fed)

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Displaying 51 - 75 of 99

CPTAC Studies 1 and 5: dissecting variability in multi-site LC-MS/MS proteomics through quality metrics and robust hierarchical multivariate statistics

February 4, 2014
Author(s)
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

Quantitative bottom-up proteomics depends on digestion conditions

December 2, 2013
Author(s)
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 differences

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

October 22, 2013
Author(s)
Yamil Simon, Mark S. Lowenthal, Lisa E. Kilpatrick, Maureen L. Sampson, Kelly H. Telu, Paul A. Rudnick, William G. Mallard, Daniel W. Bearden, Tracey B. Schock, Dmitrii V. Tchekhovskoi, Niksa Blonder, Xinjian Yan, Yuxue Liang, Yufang Zheng, William E. Wallace, 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

Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics

October 11, 2013
Author(s)
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 trypsin activity

Formation of y+10 and y+11 Ions in the Collision-Induced Dissociation of Peptide Ions

December 8, 2011
Author(s)
Lisa E. Kilpatrick, Pedatsur Neta, Xiaoyu Yang, Yamil Simon, Yuxue Liang, Stephen E. Stein
Tandem mass spectra of peptide ions, acquired in shotgun proteomic studies of selected proteins, tissues, and organisms, commonly include prominent peaks that cannot be assigned to the known fragmentation product ions (y, b, a, neutral losses). In many

Extension of ThermoML: The IUPAC Standard for Thermodynamic Data Communications (IUPAC Recommendations 2011)

September 7, 2011
Author(s)
Michael D. Frenkel, Robert D. Chirico, Vladimir Diky, Paul L. Brown, John H. Dymond, Robert N. Goldberg, Anthony R. 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 equilibria, and

Electron Ionization Mass Spectra of Alkylated Sulfabenzamides

March 30, 2011
Author(s)
Nino G. 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 very

ThermoML an XML-based Approach for Storage and Exchange of Experimental and Critically Evaluated Thermophysical and Thermochemical Property Data. 5. Speciation and Complex Equilibria

January 7, 2011
Author(s)
Michael D. Frenkel, Vladimir Diky, Robert D. Chirico, Robert N. Goldberg, Heiko Heerklotz, John E. Ladbury, David P. Remeta, John H. Dymond, Anthony R. Goodwin, Kenneth N. Marsh, William A. Wakeham, Stephen E. Stein, Paul L. Brown, Erich Koenigsberger, Peter A. Williams
ThermoML is an XML-based approach for storage and exchange of experimental and critically evaluated thermophysical and thermochemical property data. Extensions to the ThermoML schema for the representation of speciation and complex equilibria are described

Electrospray Tandem Quadrupole Fragmentation of Quinolone Drugs and Related Ions. On the Reversibility of Water Loss from Protonated Molecules

November 30, 2010
Author(s)
Pedatsur Neta, Bhaskar Godugu, Yuxue Liang, Yamil Simon, Xiaoyu Yang, Stephen E. Stein
Selected reaction monitoring (SRM) of quinolone drugs showed1 different sensitivities in aqueous solution vs. biological extract. The authors suggested formation of two singly protonated ions with different behavior, one undergoing loss of H 2O and the

Depletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics

October 1, 2010
Author(s)
Chengjian Tu, Paul A. Rudnick, Misti Y. Martinez, Kristin L. Cheek, Stephen 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 Affinity

Unique para-effect in electron ionization mass spectra of bis(perfluoroacyl) derivatives of bifunctional aminobenzenes

September 15, 2010
Author(s)
Kirill V. Tretyakov, Nino G. Todua, Roman S. Borisov, Vladimir G. Zaikin, Stephen Stein, Anzor I. Mikaia
A new kind of "para-effect" under EI conditions has been discovered for a series of bis(perfluoroacyl) derivatives of o-, m- and p- phenylendiamines, hydroxybenzeneamines and mercaptobenzeneamines of a common structure RCOX C 6H 4 NHCOR (X = NH, S, O; R =

Effect of N-Terminal Glutamic Acid and Glutamine on Fragmentation of Peptide Ions

March 27, 2010
Author(s)
Bhaskar Godugu, Pedatsur Neta, Yamil Simon, Stephen Stein
A prominent dissociation path for electrospray generated tryptic peptide ions is the dissociation of the peptide bond linking the second and third residues from the amino-terminus. The formation of the resulting b 2 and y n-2 fragments has been

Classical Trajectories and RRKM Modeling of Collisional Excitation and Dissociation of Benzylammonium and tert Butyl Benzylammonium Ions in a Quadrupole-Hexapole-Quadrupole Tandem Mass Spectrometer

March 1, 2010
Author(s)
Vadim D. Knyazev, Stephen Stein
Collision-induced dissociation of the benzylammonium and the 4-tert butyl benzylammonium ions was studied experimentally in an electrospray ionization quadrupole-hexapole-quadrupole tandem mass spectrometer. Ion fragmentation efficiencies were determined

Collisional Energy Dependence of Peptide Ion Fragmentation

March 1, 2009
Author(s)
Pedatsur Neta, Y Simon-Manso, Xiaoyu Yang, Stephen Stein
The energy dependence of fragmentation in a collision cell was measured for 2100 peptide ions derived from the digestion of twenty four common proteins. Most proteins were digested by trypsin and derived peptides were divided into several classes

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

February 11, 2009
Author(s)
Sandra Loevenich, Erich Brunner, Nichole King, Stephen Stein, Ernst Hafen, Rudolf Aebersold
Background: Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations in the reference databases used. Protein databases compiled from high quality empirical protein identifications, which are - in turn

Computer Assisted Expert Evaluation of NIST/NIH/EPA Mass Spectral Library

October 16, 2008
Author(s)
Anzor I. Mikaia, Stephen E. Stein, Vladimir G. Zaikin, D Zhu
The methods used to build a high quality, comprehensive reference library of positive ion EI mass spectra will be discussed. A description of the development of the present system of evaluation will be presented with emphasis on establishing the criteria

NIST 1. NIST/EPA/NIH Mass Spectral LibraryNIST '98 ASCII Version

October 16, 2008
Author(s)
Stephen E. Stein
NIST '98 is a fully evaluated collection of electron-ionization mass spectra. It is the product of a ten-year effort by a team of experienced mass spectrometrists in which each spectrum was examined for correctness.This has led to thousands of selections