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Search Publications by: Xiaoyu (Sara) Yang (Fed)

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Displaying 1 - 19 of 19

Comparison of N-glycopeptide to released N-glycan abundances and the influence of glycopeptide mass and charge state on N-linked glycosylation of IgG antibodies

March 7, 2024
Author(s)
Concepcion Remoroza, Meghan Burke Harris, Tytus Mak, Sergey Sheetlin, Yuri Mirokhin, Zachary Goecker, Brian T. Cooper, Mark Lowenthal, Xiaoyu (Sara) Yang, Guanghui Wang, Dmitrii V. Tchekhovskoi, Stephen E. Stein
We report the comparison of mass-spectral-based abundances of tryptic glycopeptides to fluorescence abundances of released labeled glycans and the effects of mass and charge state and in-source fragmentation on glycopeptide abundances. The primary

Determining Site-Specific Glycan Profiles of Recombinant SARS-CoV-2 Spike Proteins from Multiple Sources

August 30, 2023
Author(s)
Meghan Burke Harris, Yi Liu, Concepcion Remoroza, Yuri Mirokhin, Sergey Sheetlin, Dmitrii V. Tchekhovskoi, Guanghui Wang, Xiaoyu (Sara) Yang, Stephen E. Stein
Glycopeptide Abundance Distribution Spectra (GADS) were recently introduced as a means of representing, storing and comparing glycan profiles of intact glycopeptides. Here, using that representation, an extensive analysis is made of multiple commercial

Mass Spectral Library Methods for Analysis of Site-Specific N-Glycosylation: Application to Human Milk Proteins

September 16, 2022
Author(s)
Concepcion Remoroza, Meghan Burke Harris, Xiaoyu (Sara) Yang, Sergey Sheetlin, Yuri Mirokhin, Sanford Markey, Dmitrii V. Tchekhovskoi, Stephen E. Stein
We present a mass-spectral library-based method for analyzing site-specific N-linked protein glycosylation. Its operation and utility are illustrated by applying it to both newly measured and available proteomics data of human milk glycoproteins. It

Representing and Comparing Site-Specific Glycan Abundance Distributions of Glycoproteins

July 30, 2021
Author(s)
Concepcion Remoroza, Meghan Burke Harris, Yi Liu, Yuri Mirokhin, Dmitrii V. Tchekhovskoi, Xiaoyu (Sara) Yang, Stephen E. Stein
A method for representing and comparing distributions of N-linked glycans located at specific sites in proteins is presented. The representation takes the form of a simple mass spectrum for a given peptide sequence, with each peak corresponding to a

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

July 15, 2021
Author(s)
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

Increasing the Coverage of a Mass Spectral Library of Milk Oligosaccharides Using a Hybrid- Search-Based Bootstrapping Method and Milks from a Wide Variety of Mammals

July 8, 2020
Author(s)
Concepcion A. Remoroza, Tytus D. Mak, Yuri A. Mirokhin, Sergey L. Sheetlin, Xiaoyu Yang, Stephen E. Stein, Power L. Michael, San Andres V. Joice, Yuxue Liang
This study significantly expands both the scope and method of identification for construction of a previously reported tandem mass spectral library of 74 human milk oligosaccharides (HMOs) derived from results of LC-MS/MS experiments. In the present work

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
Author(s)
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
Author(s)
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

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 H 2O and the

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

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
Author(s)
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