Publications

Displaying 76 - 100 of 191

Analysis of Human Plasma Metabolites across Different Liquid Chromatography - Mass Spectrometry Platforms

March 15, 2016

Author(s)

Kelly H. Telu, Xinjian Yan, William E. Wallace, Stephen Stein, Yamil Simon

The development of increasingly sensitive analytical techniques has renewed interest in global metabolite profiling, i.e., the semi-quantitative monitoring of all the chemical constituents of biological fluids. In this work, global metabolite profiles of

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.

Reaction of Arylium Ions with the Collision Gas N2 in Electrospray Ionization Mass Spectrometry

January 9, 2015

Author(s)

Yuxue Liang, Pedatsur Neta, Yamil Simon, Stephen E. Stein

RATIONALE: Tandem mass spectra of many compounds contained peaks which could not arise from the precursor ion and were different in different instruments. Such peaks were found to be due to reaction of arylium ions with N2 in the collision cell. Therefore

Unexpected Peaks in Tandem Mass Spectra due to Reaction of Product Ions with Water in Mass Spectrometer Collision Cells

December 15, 2014

Author(s)

Pedatsur Neta, Mahnaz Farahani, Yamil Simon, Yuxue Liang, Xiaoyu Yang, Stephen E. Stein

While determining the fragmentation pathways of positive ions of drugs, pesticides, metabolites, and other compounds, using electrospray ionization mass spectrometry, we noticed that certain product ions react with water in the collision cell. This

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 original data files by the Automated Mass Spectral Deconvolution and Identification System (AMDIS

Loss of H2 and CO from Protonated Aldehydes in Electrospray Ionization Mass Spectrometry

September 15, 2014

Author(s)

Pedatsur Neta, Yamil Simon, Yuxue Liang, Stephen Stein

Electrospray ionization mass spectrometry of 3-formylchromones and 3-formylcoumarins shows that collision-induced dissociation of the protonated ions results in elimination of H¬¬2 as a major fragmentation route. This loss of H2 yields an unstable carbonyl

Quality Control for Building Libraries from Electrospray Ionization Tandem Mass Spectra

June 4, 2014

Author(s)

Xiaoyu (Sara) Yang, Pedatsur Neta, Stephen E. Stein

Electrospray ionization (ESI) tandem mass spectrometry coupled with liquid chromatography is a routine technique for identifying and quantifying compounds in complex mixtures. The identification step can be aided by matching acquired tandem mass spectra

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 protein. Human serum albumin (HSA) was selected for this purpose owing to its ubiquity and high level

Improved Normalization of Systematic Biases Affecting Ion Current Measurements in Label-free Proteomics Data

February 21, 2014

Author(s)

Paul A. Rudnick, Xinjian Yan, Stephen E. Stein, Xia Wang, Nell Sedransk

Systematic biases, or batch effects, in high-throughput biological datasets can be described as obscuring variabilities introduced during experimental design or analytical processing. These biases, if left unresolved, can lead to misinterpretation of

CPTAC Studies 1 and 5: dissecting variability in multi-site LC-MS/MS proteomics through quality metrics and robust hierarchical multivariate statistics

February 4, 2014

Author(s)

Stephen E. Stein, David M. Bunk, Xia Wang, Matthew Chambers, Lorenzo J. Vega-Montoto, David L. Tabb

Shotgun proteomics experiments integrate a complex sequence of processes, any of which can introduce variability. Quality metrics computed from LC-MS/MS data have relied upon identifying MS/MS scans, but a new mode for the QuaMeter software produces

Quantitative bottom-up proteomics depends on digestion conditions

December 2, 2013

Author(s)

Mark S. Lowenthal, Yuxue Liang, Karen W. Phinney, Stephen E. Stein

Accurate quantification is a fundamental requirement in the fields of proteomics and biomarker discovery, and for clinical diagnostic assays. To demonstrate the extent of quantitative variability in measurable peptide concentrations due to differences

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

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