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Search Publications by: Yuri Mirokhin (Assoc)

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Displaying 26 - 41 of 41

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

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 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