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Search Publications by: Pedatsur Neta (Fed)

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Displaying 1 - 25 of 76

Transient Phenoxyl Radicals: Formation and Properties in Aqueous Solutions

October 12, 2021
S Steenken, Pedatsur Neta
This chapter discusses the various methods of formation of phenoxyl radicals (oxidation of phenols by metal ions, by free radicals and radical cations, reaction of phenols with hydroxyl radicals, autoxidation of phenols, etc.) and the properties of

MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides

July 15, 2021
Xiaoyu (Sara) Yang, Pedatsur Neta, Yuri Mirokhin, Dmitrii V. Tchekhovskoi, Concepcion Remoroza, Meghan Burke Harris, Yuxue Liang, Sanford Markey, Stephen E. Stein
Annotating product ion peaks in tandem mass spectra is essential for evaluating spectral quality and validating peptide identification. This task is more complex for glycopeptides and is crucial for the confident determination of glycosylation sites in

Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides

November 14, 2017
Yuxue Liang, Pedatsur Neta, Xiaoyu (Sara) Yang, Stephen E. Stein
High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with 3 to 6 residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The

Interconversion of Peptide Mass Spectral Libraries Derivatized with iTRAQ or TMT Labels

July 7, 2016
Zheng Zhang, Xiaoyu Yang, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Weihua Ji, Sanford P. Markey, Pedatsur Neta, Bowen A. Michael, Stephen E. Stein
Derivatizing peptides with isobaric tags such as iTRAQ and TMT is widely employed in proteomics due to their ability to multiplex quantitative measurements. We recently made publicly available a large peptide library derived from iTRAQ 4-plex labeled

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
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

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

December 8, 2011
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

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

November 30, 2010
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

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

March 27, 2010
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

Collisional Energy Dependence of Peptide Ion Fragmentation

March 1, 2009
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

Radiation Chemistry of Phenols

October 16, 2008
Pedatsur Neta, S Steenken
This chapter summarizes the radiation chemistry of phenols. It includes studies on the radiation chemistry of phenols in aqueous solutions, in organic solvents, in solid matrices, and in the gas phase.

Consecutive Neutral Losses of H 2 O and C 2 H 4 O From N-Terminal Thr-Thr and Thr-Ser in Collision-Induced Dissociation of Protonated Peptides. Position Dependent Water Loss From Single Thr or Ser.

November 1, 2007
Pedatsur Neta, Quan-Long Pu, Xiaoyu Yang, Stephen E. Stein
A two-step neutral loss from tryptic peptides containing Thr-Thr or Thr-Ser at their N-terminus is studied. This process also requires a mobile proton (i.e., the number of charges on the peptide is greater than the number of basic amino acids) and leads to

Ionizing Radiation-Induced Destruction of Benzene and Dienes in Aqueous Media

March 28, 2006
M I. Al-Sheikhly, Dianne L. Poster, Jung-Chul An, Pedatsur Neta, Joseph Silverman, Robert E. Huie
Pulse radiolysis with spectrophotometric and conductometric detection was utilized to study the formation and reactions of radicals from benzene and dienes in aqueous solutions. The benzene OH adduct, C6H6OH, reacts with O2 (k = 3 x 108 L mol-1 s-1) in a