ArticleMolecular & cellular proteomics : MCP2010
Comparative assessment of site assignments in CID and electron transfer dissociation spectra of phosphopeptides discloses limited relocation of phosphate groups.
Article in Molecular & cellular proteomics : MCP, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 53 citations in OpenAlex.
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- Article
- Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation.The EMBO journal · 2019Article
- Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update.Analytical chemistry · 2019Review
- S- to N-Palmitoyl Transfer During Proteomic Sample Preparation.Journal of the American Society for Mass Spectrometry · 2016Article
- Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer.International journal of mass spectrometry · 2014Article
- Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation.Journal of proteomics · 2014Article
- Unblocking the sink: improved CID-based analysis of phosphorylated peptides by enzymatic removal of the basic C-terminal residue.Journal of the American Society for Mass Spectrometry · 2014Article
- Current challenges in software solutions for mass spectrometry-based quantitative proteomics.Amino acids · 2012Review
- Phosphoproteomic analysis: an emerging role in deciphering cellular signaling in human embryonic stem cells and their differentiated derivatives.Stem cell reviews and reports · 2012Review
- Database independent proteomics analysis of the ostrich and human proteome.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment.Molecular & cellular proteomics : MCP · 2011Article
- Modification site localization scoring integrated into a search engine.Molecular & cellular proteomics : MCP · 2011Article
- Confident phosphorylation site localization using the Mascot Delta Score.Molecular & cellular proteomics : MCP · 2011Article
- Enhanced characterization of singly protonated phosphopeptide ions by femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fs-LID-MS/MS).Journal of the American Society for Mass Spectrometry · 2010Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In large scale mass spectrometry-based phosphoproteomics, a current bottleneck is the unambiguous assignment of the phosphorylation site within the peptide. An additional problem is that it has been reported that under conditions wherein peptide ions are collisionally activated the phosphate group may migrate to a nearby phosphate group acceptor, thus causing ambiguity in site assignment. Here, we generated and analyzed a statistically significant number of phosphopeptides. Starting with a human cell lysate, we obtained via strong cation exchange fractionation nearly pure phosphopeptide pools from trypsin and Lys-N digestions. These pools were subjected to nano-LC-MS using an Orbitrap mass spectrometer that is equipped with both CID and electron transfer dissociation with supplemental activation (ETcaD) functionality. We configured a method to obtain sequentially both ETcaD and CID spectra for each peptide ion. We exploited the resistant nature of ETcaD toward rearrangement of phosphate groups to evaluate whether there is potentially phosphate group relocation occurring during CID. We evaluated a number of peptide and spectral annotation properties and found that for ∼75% of the sequenced phosphopeptides the assigned phosphosite was unmistakably identical for both the ETcaD and CID spectra. For the remaining 25% of the sequenced phosphopeptides, we also did not observe evident signs of relocation, but these peptides exhibited signs of ambiguity in site localization, predominantly induced by factors such as poor fragmentation, sequences causing inefficient fragmentation, and generally poor spectrum quality. Our data let us derive the conclusion that both for trypsin- and Lys-N-generated peptides there is little relocation of phosphate groups occurring during CID.
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