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Publications

Search Publications by

Yamil Simon (Fed)

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Displaying 1 - 21 of 21

Metabolomics Test Materials for Quality Control: A Study of a Urine Materials Suite

November 7, 2019
Author(s)
Dan Bearden, David A. Sheen, Yamil Simon, Bruce A. Benner Jr., Werickson Fortunato de Carvalho Rocha, Niksa Blonder, Katrice A. Lippa, Richard Beger, Laura Schnackenberg, Jinchun Sun, Khyati Mehta, Amrita Cheema, Haiwei Gu, Ramesh Marupaka, Nagana Gowda, Daniel Raftery
There is a lack of experimental reference materials and standards for metabolomics measurements, such as urine, plasma, and other human fluid samples. Reasons include difficulties with supply, distribution, and dissemination of information about the

Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids. Building a Spectral Library of Recurrent Spectra for Urine Analysis.

August 19, 2019
Author(s)
Yamil Simon, Ramesh Marupaka, Xinjian Yan, Yuxue Liang, Kelly H. Telu, Yuri A. Mirokhin, Stephen E. Stein
A large fraction of ions observed in electrospray liquid chromatography-mass spectrometry (LC-MS) experiments of biological samples remain unidentified. One the main reasons for this is that spectral libraries of pure compounds fail to account for the

Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids. Building a Spectral Library of Recurrent Spectra for Urine Analysis

August 19, 2019
Author(s)
Yamil Simon, Ramesh Marupaka, Xinjian Yan, Yuxue Liang, Kelly H. Telu, Yuri A. Mirokhin
A large fraction of ions observed in electrospray liquid chromatography-mass spectrometry (LC- MS) experiments of biological samples remain unidentified. One the main reasons for this is that spectral libraries of pure compounds fail to account for the

Cross-Ring Fragmentation Patterns in the Tandem Mass Spectra of Underivatized Sialylated Oligosaccharides and Their Special Suitability for Spectrum Library Searching

December 18, 2018
Author(s)
M. L. De Leoz, Yamil Simon, Robert J. Woods, Stephen E. Stein
Reference spectral library searching, while widely used to identify compounds in other areas of mass spectrometry, is not commonly used in glycomics. Building on a study by Cotter and coworkers on analysis of sialylated oligosaccharides using atmospheric

Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods

September 3, 2015
Author(s)
Yamil Simon, Daniel Abate-Pella, Dana M. Freund, Yan Ma, Adrian Hegeman, Yan Ma, Tobias Kind, O Fiehn, Birgit Beck, Emma L. Schymanski, Corey D. Broeckling, David V. Huhman, Lloyd W. Summer, Oleg V. Krokhin, Dwight R. Stoll
Identification of small molecules by liquid chromatography-mass spectrometry (LC-MS) could be greatly improved if the chromatographic retention information could be used along with mass spectral information to narrow down the lists of potential identities

Pairwise Alignment of Chromatograms using a Fisher-Rao Metric

September 2, 2014
Author(s)
William E. Wallace, Anuj Srivastava, Kelly H. Telu, Yamil Simon
A new approach to aligning chromatograms is introduced and applied to examples of metabolite identification by liquid chromatography mass spectrometry (LC MS). A square root representation of the chromatogram’s derivative coupled with a Fisher Rao

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

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

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 H2O and the

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 b2 and yn-2 fragments has been rationalized