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Search Publications by: Dmitrii V. Tchekhovskoi (Fed)

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Displaying 1 - 22 of 22

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

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

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

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

Combining fragment ion and neutral loss matching during mass spectral library searching: A new general-purpose algorithm applicable to illicit drug identification

November 20, 2017
Author(s)
Arun S. Moorthy, William E. Wallace, Anthony J. Kearsley, Dmitrii V. Tchekhovskoi, Stephen E. Stein
A mass spectral library search algorithm that identifies compounds that differ from library compounds by a single ‘inert’ structural component is described. This algorithm, the Hybrid Similarity Search, generates a similarity score based on matching both

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

Mass Spectral Library Quality Assurance by Inter-Library Comparison

April 2, 2017
Author(s)
William E. Wallace, Weihua Ji, Dmitrii V. Tchekhovskoi, Karen W. Phinney, Stephen E. Stein
A method to discover and correct errors in mass spectral libraries is described. Comparing across a set of highly curated reference libraries compounds that have the same chemical structure quickly identifies entries that are outliers. In cases where three

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 Markey, Yuri Mirokhin, Xinjian Yan, Dmitrii Tchekhovskoi, Stephen 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

InChI, the IUPAC International Chemical Identifier

April 15, 2015
Author(s)
Stephen R. Heller, Alan McNaught, Igor Pletnev, Stephen Stein, Dmitrii Tchekhovskoi
This paper documents the design, layout and algorithms of the IUPAC International Chemical Identifier, InChI.

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

An Open Standard for Chemical Structure Representation: The IUPAC Chemical Identifier

September 1, 2003
Author(s)
Stephen E. Stein, Stephen R. Heller, Dmitrii V. Tchekhovskoi
IUPAC has long been involved in the development of systematic and standard procedures for naming chemical substances on the basis of their structure. The resulting rules of nomenclature, while covering almost all compounds, were designed for text-based

The IUPAC Chemical Identifier

July 1, 2002
Author(s)
Stephen E. Stein, Stephen R. Heller, Dmitrii V. Tchekhovskoi
The author presented two talks at the IUPAC/CAS conference of Chemical identifiers and XML in Chemistry, on July 1, 2002 in Columbus Ohio. He will be sending powerpoint presentations of these talks, both concerning on-going projects at NIST, to IUPAC for

The Critical Evaluation of a Comprehensive Mass Spectral Library

August 1, 1999
Author(s)
P Ausloos, C L. Clifton, S G. Lias, Anzor I. Mikaia, Stephen Stein, Dmitrii Tchekhovskoi, O D. Sparkman, Vladimir G. Zaikin, D Zhu
A description of the methods used to build a high quality, comprehensive reference library of electron-ionization mass spectra is presented. Emphasis is placed on the most challenging part of this project the improvement of quality by expert evaluation

The critical evaluation of a comprehensive mass spectral library

March 15, 1999
Author(s)
C L. Clifton, S G. Lias, Anzor I. Mikaia, Stephen Stein, Dmitrii Tchekhovskoi, O D. Sparkman, Vladimir G. Zaikin, Damo Zhu
A description of methods used to build a high quality, comprehensive reference library of EI mass spectra is presented

Quality Control Procedures for the NIST/EPA/NIH Mass Spectral Library

May 31, 1998
Author(s)
C L. Clifton, S G. Lias, Anzor I. Mikaia, O D. Sparkman, Stephen Stein, Dmitrii Tchekhovskoi, Damo Zhu, Vladimir G. Zaikin
The goal of quality control procedures is to produce the best possible spectra for library searching. The role of a panel of data evaluators is presented, and the plans for further improvements of the NIST/EPA/NIH mass spectral library is presented.