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Search Publications by: Yuxue Liang (Fed)

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Displaying 1 - 25 of 47

Molecular Oxygen (O2) Artifacts in Tandem Mass Spectra

November 20, 2024
Author(s)
Yuxue Liang, Pedatsur Neta, Xiaoyu (Sara) Yang, Hugo Garraffo, Tallat Bukhari, Yi Liu, Stephen Stein
The NIST 2023 tandem mass spectral library contains 1,832,086 spectra of positive ions and 541,978 of negative ions from 51,501 compounds. Peak annotation plays an important role in spectrum evaluation. While most fragment ions are formed by neutral losses

On the challenge of unambiguous identification of fentanyl analogs: exploring measurement diversity using standard reference mass spectral libraries

July 11, 2023
Author(s)
Arun Moorthy, Edward Erisman, Anthony J. Kearsley, Yuxue Liang, Edward Sisco, William E. Wallace
Fentanyl analogs are a class of designer drugs that are particularly challenging to unambiguously identify due to the mass spectral and retention time similarities of unique compounds. In this paper, we use agglomerative hierarchical clustering to explore

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

Comprehensive Analysis of Tryptic Peptides Arising from Disulfide Linkages in NISTmAb and Their Use for Developing a Mass Spectral Library

June 22, 2021
Author(s)
Qian Dong, Xinjian Yan, Yuxue Liang, Sanford Markey, Sergey L. Sheetlin, Concepcion Remoroza, William E. Wallace, Stephen Stein
This work presents methods for identifying and then creating a mass spectral library for disulfide-linked peptides originating from the NISTmAb. Analysis involved both partially- reduced and non-reduced proteins under neutral and weakly basic conditions

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

Sensitive Method for the Confident Identification of Genetically Variant Peptides in Human Hair

October 31, 2019
Author(s)
Zheng Zhang, Meghan Burke, William E. Wallace, Yuxue Liang, Sergey L. Sheetlin, Yuri Mirokhin, Dmitrii Tchekhovskoi, Stephen Stein
Recent reports have demonstrated that genetically variant peptides (GVPs) derived from human hair shaft proteins can be used to differentiate individuals of different biogeographic origin (Parker, G.J.; et al. PLos One. 2016, e0160653). We report a direct

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 18, 2019
Author(s)
Yamil Simon, Ramesh Marupaka, Xinjian Yan, Yuxue Liang, Kelly H. Telu, Yuri Mirokhin, Stephen E. Stein
A large fraction of ions observed in electrospray liquid chromatography–mass spectrometry (LC–ESI-MS) experiments of biological samples remain unidentified. One of the main reasons for this is that spectral libraries of pure compounds fail to account for

The NISTmAb Tryptic Peptide Spectral Library for Monoclonal Antibody Characterization

March 6, 2018
Author(s)
Qian Dong, Yuxue Liang, Xinjian Yan, Sanford Markey, Yuri Mirokhin, Dmitrii V. Tchekhovskoi, Tallat H. Bukhari, Stephen E. Stein
We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of a therapeutic monoclonal antibody. The NISTmAb library is a unique reference peptide spectral library developed from a total of six