Publications

Displaying 1 - 14 of 14

Mass Spectral Library of Acylcarnitines Derived from Human Urine in Human Urine

April 9, 2020

Author(s)

Xinjian Yan, Sanford P. Markey, Ramesh Marupaka, Qian Dong, Brian T. Cooper, Yuri A. Mirokhin, William E. Wallace, Stephen E. Stein

We describe the creation of a mass spectral library of acylcarnitines and conjugated acylcarnitines from the LCMS/MS analysis of six NIST urine reference

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

October 31, 2019

Author(s)

Zheng Zhang, Meghan C. Burke, William E. Wallace, Yuxue Liang, Sergey L. Sheetlin, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Stephen E. Stein

Recent reports have demonstrated that genetically variant peptides (GVPs) derived from human hair shaft proteins can be used to differentiate individuals of

Hybrid search: a method for identifying metabolites absent from tandem mass spectrometry libraries

October 10, 2019

Author(s)

Brian T. Cooper, Xinjian Yan, Yamil Simon, Dmitrii V. Tchekhovskoi, Yuri A. Mirokhin, Stephen E. Stein

Metabolomics has a critical need for better tools for mass spectral identification. Common metabolites may be identified by searching libraries of tandem mass

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

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

False Discovery Rate Estimation for Hybrid Mass Spectral Library Search Identifications in Bottom-up Proteomics

July 31, 2019

Author(s)

Meghan C. Burke, Zheng Zhang, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Yuxue Liang, Stephen E. Stein

We present a method for FDR estimation of mass spectral library search identifications made by a recently developed method for peptide identification, 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

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

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

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

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

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

Creation of Libraries of Recurring Mass Spectra from Large Data Sets assisted by a Dual-Column Workflow

September 18, 2014

Author(s)

William G. Mallard, Stephen E. Stein, Halket M. John, Yuri A. Mirokhin, Nirina Rabe Andriamaharavo

An analytical methodology has been developed for extracting recurrent unidentified spectra (RUS) from large GC/MS data sets. Spectra were first extracted from

Tandem Mass Spectral Libraries of Peptides in Digests of Individual Proteins: Human Serum Albumin

June 2, 2014

Author(s)

Qian Dong, Xinjian Yan, Lisa E. Kilpatrick, Yuxue Liang, Yuri A. Mirokhin, Jeri S. Roth, Stephen E. Stein

This work presents a method for creating a mass spectral library containing tandem spectra identifiable peptide ions in the tryptic digestion of a single

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