ArticleMolecular & cellular proteomics : MCP2015
The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD).
Article in Molecular & cellular proteomics : MCP, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
37 citing papers in PubMed, 64 citations in OpenAlex.
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- Instrumentation at the Leading Edge of Proteomics.Analytical chemistry · 2024Review
- Phosphorothioate RNA Analysis by NETD Tandem Mass Spectrometry.Molecular & cellular proteomics : MCP · 2024Article
- Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides.Journal of proteome research · 2023Article
- Potential of Negative-Ion-Mode Proteomics: An MS1-Only Approach.Journal of proteome research · 2023Article
- N-glycoproteomics of brain synapses and synaptic vesicles.Cell reports · 2023Article
- Characterization of Treponema denticola Major Surface Protein (Msp) by Deletion Analysis and Advanced Molecular Modeling.Journal of bacteriology · 2022Article
- High-Resolution Demultiplexing (HRdm) Ion Mobility Spectrometry-Mass Spectrometry for Aspartic and Isoaspartic Acid Determination and Screening.Analytical chemistry · 2022Article
- The many ways that nature has exploited the unusual structural and chemical properties of phosphohistidine for use in proteins.The Biochemical journal · 2021Review
- A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics.Molecular & cellular proteomics : MCP · 2021Review
- Protein identification by 3D OrbiSIMS to facilitate in situ imaging and depth profiling.Nature communications · 2020Article
- Optical Fiber-Enabled Photoactivation of Peptides and Proteins.Analytical chemistry · 2020Article
- Maximizing binary interactome mapping with a minimal number of assays.Nature communications · 2019Article
- Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications.Molecular & cellular proteomics : MCP · 2019Article
- Dual Polarity Ion Confinement and Mobility Separations.Journal of the American Society for Mass Spectrometry · 2019Article
- Gas-Phase Hydrogen/Deuterium Scrambling in Negative-Ion Mode Tandem Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2019Article
- Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update.Analytical chemistry · 2019Review
- Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure.Mass spectrometry reviews · 2018Review
- Replacing HChemical science · 2018Article
- Comparison of Collisional and Electron-Based Dissociation Modes for Middle-Down Analysis of Multiply Glycosylated Peptides.Journal of the American Society for Mass Spectrometry · 2018Article
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9 authors at 1 institution in 1 country.
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Abstract
The field of proteomics almost uniformly relies on peptide cation analysis, leading to an underrepresentation of acidic portions of proteomes, including relevant acidic posttranslational modifications. Despite the many benefits negative mode proteomics can offer, peptide anion analysis remains in its infancy due mainly to challenges with high-pH reversed-phase separations and a lack of robust fragmentation methods suitable for peptide anion characterization. Here, we report the first implementation of activated ion negative electron transfer dissociation (AI-NETD) on the chromatographic timescale, generating 7,601 unique peptide identifications from Saccharomyces cerevisiae in single-shot nLC-MS/MS analyses of tryptic peptides-a greater than 5-fold increase over previous results with NETD alone. These improvements translate to identification of 1,106 proteins, making this work the first negative mode study to identify more than 1,000 proteins in any system. We then compare the performance of AI-NETD for analysis of peptides generated by five proteases (trypsin, LysC, GluC, chymotrypsin, and AspN) for negative mode analyses, identifying as many as 5,356 peptides (1,045 proteins) with LysC and 4,213 peptides (857 proteins) with GluC in yeast-characterizing 1,359 proteins in total. Finally, we present the first deep-sequencing approach for negative mode proteomics, leveraging offline low-pH reversed-phase fractionation prior to online high-pH separations and peptide fragmentation with AI-NETD. With this platform, we identified 3,467 proteins in yeast with trypsin alone and characterized a total of 3,730 proteins using multiple proteases, or nearly 83% of the expressed yeast proteome. This work represents the most extensive negative mode proteomics study to date, establishing AI-NETD as a robust tool for large-scale peptide anion characterization and making the negative mode approach a more viable platform for future proteomic studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.