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Publications

Search Publications by Yuri Mirokhin

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Displaying 1 - 17 of 17

Representing and Comparing Site-Specific Glycan Abundance Distributions of Glycoproteins

July 30, 2021
Author(s)
Concepcion Remoroza, Meghan Burke, Yi Liu, Yuri Mirokhin, Dmitrii Tchekhovskoi, Xiaoyu Yang, Stephen 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 Yang, Pedatsur Neta, Yuri Mirokhin, Dmitrii Tchekhovskoi, Concepcion Remoroza, Meghan Burke, Yuxue Liang, Sanford Markey, Stephen 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

Mass Spectral Library of Acylcarnitines Derived from Human Urine

April 8, 2020
Author(s)
Xinjian Yan, Sanford Markey, Ramesh Marupaka, Qian Dong, Brian T. Cooper, Yuri Mirokhin, William E. Wallace, Stephen Stein
We describe the creation of a mass spectral library of acylcarnitines and conjugated acylcarnitines from the LC–MS/MS analysis of six NIST urine reference materials. To recognize acylcarnitines, we conducted in-depth analyses of fragmentation patterns of

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 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

Creating a Mass Spectral Reference Library for Oligosaccharides in Milk

July 3, 2018
Author(s)
Concepcion A. Remoroza, Tytus D. Mak, M. L. De Leoz, Yuri A. Mirokhin, Stephen E. Stein
We report the development and availability of a mass spectral reference library for oligosaccharides in human milk. This represents a new variety of spectral library that includes consensus spectra of compounds annotated through various data analysis

The NISTmAb Tryptic Peptide Spectral Library for Monoclonal Antibody Characterization

February 9, 2018
Author(s)
Qian Dong, Yuxue Liang, Xinjian Yan, Sanford P. Markey, Yuri A. 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

Reverse and Random Decoy Methods for False Discovery Rate Estimation in High Mass Accuracy Peptide Spectral Library Searches

February 2, 2018
Author(s)
Zheng Zhang, Meghan C. Burke, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Sanford P. Markey, Wen Yu, Raghothama Chaerkady, Sonja Hess, Stephen E. Stein
Spectral library searching (SLS) is an attractive alternative to sequence database searching (SDS) for peptide identification due to its speed, sensitivity, and ability to include any selected mass spectra. However, SLS does not have a widely tested and

The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics

April 3, 2017
Author(s)
Meghan C. Burke, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Sanford P. Markey, Stephen E. Stein, Jenny Heidbrink Thompson, Christopher Larkin
We present a mass spectral library based method to identify tandem mass spectra of peptides that contain unanticipated modifications and amino acid variants. We describe this as a ‘hybrid’ method since it combines matching both ion m/z and mass losses. 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

A Description of the Clinical Proteomics Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline

February 10, 2016
Author(s)
Jeri S. Roth, Paul A. Rudnick, Sanford P. Markey, Yuri A. Mirokhin, Xinjian Yan, Dmitrii V. Tchekhovskoi, Stephen E. Stein, Nathan J. Edwards, Ratna R. Thangudu, Karen A. Ketchum, Christopher R. Kinsinger, Mehdi Mesri, Henry Rodriguez
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics datasets from the mass spectrometric interrogation of tumor samples previously studied by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and