ArticleAnalytica chimica acta2017
Improving data quality and preserving HCD-generated reporter ions with EThcD for isobaric tag-based quantitative proteomics and proteome-wide PTM studies.
Article in Analytica chimica acta, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 28 citations in OpenAlex.
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- Mapping the O-GlcNAc Modified Proteome: Applications for Health and Disease.Frontiers in molecular biosciences · 2022Review
- Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging.Expert review of proteomics · 2021Review
- Developing mass spectrometry for the quantitative analysis of neuropeptides.Expert review of proteomics · 2021Review
- Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway.Scientific reports · 2021Article
- Mass Spectrometry-based Proteomics and Glycoproteomics in COVID-19 Biomarkers Identification: A Mini-review.Journal of analysis and testing · 2021Review
- Ion Activation Methods for Peptides and Proteins.Analytical chemistry · 2020Review
- Finding the Sweet Spot in ERLIC Mobile Phase for Simultaneous Enrichment of N-Glyco and Phosphopeptides.Journal of the American Society for Mass Spectrometry · 2019Article
- Sample Multiplexing Strategies in Quantitative Proteomics.Analytical chemistry · 2019Review
- Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Mass spectrometry (MS)-based isobaric labeling has undergone rapid development in recent years due to its capability for high throughput quantitation. Apart from its originally designed use with collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD), isobaric tagging technique could also work with electron-transfer dissociation (ETD), which provides complementarity to CID and is preferred in sequencing peptides with post-translational modifications (PTMs). However, ETD suffers from long reaction time, reduced duty cycle and bias against peptides with lower charge states. In addition, common fragmentation mechanism in ETD results in altered reporter ion production, decreased multiplexing capability, and even loss of quantitation capability for some of the isobaric tags, including custom-designed dimethyl leucine (DiLeu) tags. Here, we demonstrate a novel electron-transfer/higher-energy collision dissociation (EThcD) approach that preserves original reporter ion channels, mitigates bias against lower charge states, improves sensitivity, and significantly improves data quality for quantitative proteomics and proteome-wide PTM studies. Systematic optimization was performed to achieve a balance between data quality and sensitivity. We provide direct comparison of EThcD with ETD and HCD for DiLeu- and TMT-labeled HEK cell lysate and IMAC enriched phosphopeptides. Results demonstrate improved data quality and phosphorylation localization accuracy while preserving sufficient reporter ion production. Biological studies were performed to investigate phosphorylation changes in a mouse vascular smooth muscle cell line treated with four different conditions. Overall, EThcD exhibits superior performance compared to conventional ETD and offers distinct advantages compared to HCD in isobaric labeling based quantitative proteomics and quantitative PTM studies.
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