David D. Shteynberg

发表

Eduardo Eyras, Paul Flicek, Stylianos E. Antonarakis, 2005, BMC Bioinformatics.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Colin N. Dewey, Paul E. Boardman, David D. Shteynberg, 2004, Nature.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Lisa M. D'Souza, Colin N. Dewey, Martin S. Taylor, 2004, Nature.

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates*

Natalie I. Tasman, David D. Shteynberg, Henry H. N. Lam, 2011, Molecular & Cellular Proteomics.

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

David D. Shteynberg, U. Kusebauch, R. Moritz, 2015, Journal of proteome research.

A guided tour of the Trans‐Proteomic Pipeline

Natalie I. Tasman, David D. Shteynberg, Daniel B. Martin, 2010, Proteomics.

Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides*

David D. Shteynberg, Samuel L. Bader, L. Hood, 2015, Molecular & Cellular Proteomics.

Trans‐Proteomic Pipeline, a standardized data processing pipeline for large‐scale reproducible proteomics informatics

Luis Mendoza, Eric W Deutsch, Robert L Moritz, 2015, Proteomics. Clinical applications.

A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS

David D. Shteynberg, Samuel L. Bader, N. Baliga, 2020, Scientific data.

Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N.

David D. Shteynberg, Daniel B. Martin, J. Eng, 2009, Journal of proteome research.

State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.

Eric W Deutsch, Gilbert S Omenn, Robert L Moritz, 2014, Journal of proteome research.

Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells

David D. Shteynberg, U. Kusebauch, R. Moritz, 2014, Front. Microbiol..

The Microvesicle Component of HIV-1 Inocula Modulates Dendritic Cell Infection and Maturation and Enhances Adhesion to and Activation of T Lymphocytes

David D. Shteynberg, U. Kusebauch, R. Moritz, 2013, PLoS pathogens.

reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

David D. Shteynberg, R. Moritz, E. Deutsch, 2015, Journal of The American Society for Mass Spectrometry.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

Chris Sander, Eric W. Deutsch, Emek Demir, 2016, Cell.

Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline.

David D. Shteynberg, M. MacCoss, R. Moritz, 2023, Journal of proteome research.

Oncogenic H-Ras Reprograms Madin-Darby Canine Kidney (MDCK) Cell-derived Exosomal Proteins Following Epithelial-Mesenchymal Transition*

Eugene A. Kapp, David D. Shteynberg, U. Kusebauch, 2013, Molecular & Cellular Proteomics.

Oncogenic HRas reprograms Madin-Darby canine kidney ( MDCK ) cell-derived exosomal proteins following epithelial-mesenchymal transition

Eugene A. Kapp, David D. Shteynberg, U. Kusebauch, 2013 .

Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis.

Alexey I Nesvizhskii, Ruedi Aebersold, Mingliang Ye, 2006, Journal of proteome research.

iProphet: improved validation of peptide identification in shotgun proteomics

Henry H N Lam, Ruedi Aebersold, Alexey I. Nesvizhskii, 2008 .

iProphet: Improved statistical validation of peptide and protein identifications in shotgun proteomics

Henry H N Lam, Luis Mendoza, Ruedi Aebersold, 2011 .

iProphet: A new tool for combining PeptideProphet results from multiple search engines improves spectrum validation

Henry H N Lam, Ruedi Aebersold, Alexey I. Nesvizhskii, 2008 .

Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction*

Alexey I Nesvizhskii, Alexander V Ratushny, John D Aitchison, 2010, Molecular & Cellular Proteomics.

Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.

David D. Shteynberg, R. Moritz, J. Eng, 2023, Journal of proteome research.

Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project.

Magnus Palmblad, Nuno Bandeira, Bin Xia, 2020, Journal of proteome research.

PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline

Eric W. Deutsch, Luis Mendoza, Mukul Kumar Midha, 2019, bioRxiv.

A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry.

Luis Mendoza, Eric W Deutsch, Robert L Moritz, 2018, Journal of proteome research.

Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.

Luis Mendoza, Eric W Deutsch, Robert L Moritz, 2018, Journal of proteome research.

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

Luis Mendoza, Pierre-Alain Binz, Eric W Deutsch, 2016, Journal of proteome research.

Processing Shotgun Proteomics Data on the Amazon Cloud with the Trans-Proteomic Pipeline*

Luis Mendoza, Eric W Deutsch, Robert L Moritz, 2014, Molecular & Cellular Proteomics.

Combining Results of Multiple Search Engines in Proteomics*

Eric W. Deutsch, Alexey I. Nesvizhskii, Robert L. Moritz, 2013, Molecular & Cellular Proteomics.

Combining Results of Multiple Search Engines

Alexey I. Nesvizhskii, Robert L. Moritz, David Shteynberg, 2013 .

MaRiMba: a software application for spectral library-based MRM transition list assembly.

Luis Mendoza, Ruedi Aebersold, Eric W Deutsch, 2009, Journal of proteome research.

Trans‐Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets

Luis Mendoza, Ruedi Aebersold, Eric W Deutsch, 2010, Proteomics.

Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing.

Manimozhiyan Arumugam, David Shteynberg, David D. Shteynberg, 2004, Genome research.

Resource Human SRMAtlas : A Resource of Targeted Assays to Quantify the Complete Human Proteome Graphical Abstract Highlights

David D. Shteynberg, Henry H. N. Lam, L. Hood, 2016 .

An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results

Luis Mendoza, Eric W Deutsch, Robert L Moritz, 2016, Journal of The American Society for Mass Spectrometry.

Software pipeline and data analysis for MS/MS proteomics: the trans-proteomic pipeline.

Andrew Keller, David Shteynberg, David D. Shteynberg, 2011, Methods in molecular biology.

Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet*

Andrew Keller, Robert L Moritz, Samuel L Bader, 2015, Molecular & Cellular Proteomics.

Processing Shotgun Proteomics Data on the Amazon Cloud with the Trans-Proteomic Pipeline*

David D. Shteynberg, R. Moritz, E. Deutsch, 2014, Molecular & Cellular Proteomics.

Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N.

David D. Shteynberg, Daniel B. Martin, J. Eng, 2009, Journal of proteome research.

A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS

David D. Shteynberg, N. Baliga, U. Kusebauch, 2023, Scientific data.