ArticleProteomics2011
Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides.
Article in Proteomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed.
- Trapped Ion Mobility Spectrometry, Ultraviolet Photodissociation, and Time-of-Flight Mass Spectrometry for Gas-Phase Peptide Isobars/Isomers/Conformers Discrimination.Journal of the American Society for Mass Spectrometry · 2022Article
- Coupling 193 nm Ultraviolet Photodissociation and Ion Mobility for Sequence Characterization of Conformationally-Selected Peptides.Journal of the American Society for Mass Spectrometry · 2020Article
- Phosphoproteomics analysis of male and female Schistosoma mekongi adult worms.Scientific reports · 2019Article
- Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure.Analytical chemistry · 2019Review
- Gas-Phase Fragmentation Behavior of Oxidized Prenyl Peptides by CID and ETD Tandem Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2017Article
- Common errors in mass spectrometry-based analysis of post-translational modifications.Proteomics · 2016Review
- Review
- Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation.Journal of proteomics · 2014Article
- Reliable determination of site-specific in vivo protein N-glycosylation based on collision-induced MS/MS and chromatographic retention time.Journal of the American Society for Mass Spectrometry · 2014Article
- Proteomic approaches for site-specific O-GlcNAcylation analysis.Bioanalysis · 2014Review
- Phosphopeptide enrichment with TiO2-modified membranes and investigation of tau protein phosphorylation.Analytical chemistry · 2013Article
- Unambiguous phosphosite localization using electron-transfer/higher-energy collision dissociation (EThcD).Journal of proteome research · 2013Article
- Peptide identification by tandem mass spectrometry with alternate fragmentation modes.Molecular & cellular proteomics : MCP · 2012Review
- Charge state coalescence during electrospray ionization improves peptide identification by tandem mass spectrometry.Journal of the American Society for Mass Spectrometry · 2012Article
- Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Electron transfer dissociation mass spectrometry in proteomics.Proteomics · 2012Review
- Learning from decoys to improve the sensitivity and specificity of proteomics database search results.PloS one · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
CID has become a routine method for fragmentation of peptides in shotgun proteomics, whereas electron transfer dissociation (ETD) has been described as a preferred method for peptides carrying labile PTMs. Though both of these fragmentation techniques have their obvious advantages, they also have their own drawbacks. By combining data from CID and ETD fragmentation, some of these disadvantages can potentially be overcome because of the complementarity of fragment ions produced. To evaluate alternating CID and ETD fragmentation, we analyzed a complex mixture of phosphopeptides on an LTQ-Orbitrap mass spectrometer. When the CID and ETD-derived spectra were searched separately, we observed 2504, 491, 2584, and 3249 phosphopeptide-spectrum matches from CID alone, ETD alone, decision tree-based CID/ETD, and alternating CID and ETD, respectively. Combining CID and ETD spectra prior to database searching should, intuitively, be superior to either method alone. However, when spectra from the alternating CID and ETD method were merged prior to database searching, we observed a reduction in the number of phosphopeptide-spectrum matches. The poorer identification rates observed after merging CID and ETD spectra are a reflection of a lack of optimized search algorithms for carrying out such searches and perhaps inherent weaknesses of this approach. Thus, although alternating CID and ETD experiments for phosphopeptide identification are desirable for increasing the confidence of identifications, merging spectra prior to database search has to be carefully evaluated further in the context of the various algorithms before adopting it as a routine strategy.
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