David Shteynberg
YOU?
Author Swipe
View article: Assessment of Reported Error Rates in Crosslinking Mass Spectrometry
Assessment of Reported Error Rates in Crosslinking Mass Spectrometry Open
We benchmarked eight software tools in crosslinking mass spectrometry (MS) to evaluate their accuracy in detecting protein-protein interactions. Whereas about half performed reliably, others reported up to 31-fold more false interactions t…
View article: Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme research
Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme research Open
Lyme disease is caused by an infection with the spirochete Borrelia burgdorferi, and is the most common vector-borne disease in North America. B. burgdorferi isolates harbor extensive genomic and proteomic variability and further compariso…
View article: Detection and Quantification of Drug–Protein Adducts in Human Liver
Detection and Quantification of Drug–Protein Adducts in Human Liver Open
Covalent protein adducts formed by drugs or their reactive metabolites are risk factors for adverse reactions, and inactivation of cytochrome P450 (CYP) enzymes. Characterization of drug-protein adducts is limited due to lack of methods id…
View article: Carafe enables high quality <i>in silico</i> spectral library generation for data-independent acquisition proteomics
Carafe enables high quality <i>in silico</i> spectral library generation for data-independent acquisition proteomics Open
Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of …
View article: A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS
A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS Open
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori genera…
View article: Borrelia PeptideAtlas: A proteome resource of common<i>Borrelia burgdorferi</i>isolates for Lyme research
Borrelia PeptideAtlas: A proteome resource of common<i>Borrelia burgdorferi</i>isolates for Lyme research Open
Lyme disease, caused by an infection with the spirochete Borrelia burgdorferi , is the most common vector-borne disease in North America. B. burgdorferi strains harbor extensive genomic and proteomic variability and further comparison is k…
View article: Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers
Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers Open
The analysis of protein phosphorylation site identification by mass spectrometry-based methods continues to improve with increased efficiency at multiple points of the pipeline including affinity isolation, sample handling with automated p…
View article: Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers
Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers Open
The analysis of protein phosphorylation site identification by mass spectrometry-based methods continues to improve with increased efficiency at multiple points of the pipeline including affinity isolation, sample handling with automated p…
View article: Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite Open
The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet and ProteinProphet, were published 20 years ago. The current release provides a…
View article: Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline
Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline Open
Fragmentation ion spectral analysis of chemically cross-linked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak vers…
View article: The Trans-Proteomic Pipeline: Robust Mass Spectrometry-based Proteomics Data Analysis Suite
The Trans-Proteomic Pipeline: Robust Mass Spectrometry-based Proteomics Data Analysis Suite Open
The Trans-Proteomic Pipeline mass spectrometry data analysis suite has been in continual development and refinement since its first tools PeptideProphet and ProteinProphet were published twenty years ago. The current release provides a lar…
View article: A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS
A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS Open
Data-Independent Acquisition (DIA) is a method to improve consistent identification and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted data analysis strategy in DIA relies on spectral assay libraries …
View article: Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project
Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project Open
Mass spectrometry has greatly improved the analysis of phosphorylation events in complex biological systems and on a large scale. Despite considerable progress, the correct identification of phosphorylated sites, their quantification, and …
View article: PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline
PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline Open
Spectral matching sequence database search engines commonly used on mass spectrometry-based proteomics experiments excel at identifying peptide sequence ions, and in addition, possible sequence ions carrying post-translational modification…
View article: A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry
A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry Open
Thrombospondin type 1 repeats (TSRs), small adhesive protein domains with a wide range of functions, are usually modified with O-linked fucose, which may be extended to O-fucose-β1,3-glucose. Collision-induced dissociation (CID) spectra of…
View article: Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper
Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper Open
Bottom-up proteomics relies on the proteolytic or chemical cleavage of proteins into peptides, the identification of those peptides via mass spectrometry, and the mapping of the identified peptides back to the reference proteome to infer w…
View article: Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics
Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics Open
The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources fro…
View article: An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results
An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results Open
Protein-protein interactions are an important element in the understanding of protein function, and chemical cross-linking shotgun mass spectrometry is rapidly becoming a routine approach to identify these specific interfaces and topograph…
View article: Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides
Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides Open
Posttranslational modifications of proteins play an important role in biology. For example, phosphorylation is a key component in signal transduction in all three domains of life, and histones can be modified in such a variety of ways that…
View article: reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra
reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra Open
Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often iso…
View article: State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet
State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet Open
The Human PeptideAtlas is a compendium of the highest quality peptide identifications from over 1000 shotgun mass spectrometry proteomics experiments collected from many different laboratories, all reanalyzed through a uniform processing p…
View article: Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet
Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet Open
Proteomics by mass spectrometry technology is widely used for identifying and quantifying peptides and proteins. The breadth and sensitivity of peptide detection have been advanced by the advent of data-independent acquisition mass spectro…
View article: Trans‐Proteomic Pipeline, a standardized data processing pipeline for large‐scale reproducible proteomics informatics
Trans‐Proteomic Pipeline, a standardized data processing pipeline for large‐scale reproducible proteomics informatics Open
Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular…