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Search Publications by: Stephen E. Stein (Fed)

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Displaying 26 - 50 of 99

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

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

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

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

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.