ReviewMolecular & cellular proteomics : MCP2012
Peptide identification by tandem mass spectrometry with alternate fragmentation modes.
Review in Molecular & cellular proteomics : MCP, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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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
25 citing papers in PubMed.
- Synergistic Arg-C Ultra and Lys-C Digestion for Quantitative Proteomics.bioRxiv : the preprint server for biology · 2025Article
- Decoding Neuropeptide Complexity: Advancing Neurobiological Insights from Invertebrates to Vertebrates through Evolutionary Perspectives.ACS chemical neuroscience · 2025Review
- Potential of MALDI-TOF MS biotyping to detect deltamethrin resistance in the dengue vector Aedes aegypti.PloS one · 2024Article
- Accurate Prediction of y Ions in Beam-Type Collision-Induced Dissociation Using Deep Learning.Analytical chemistry · 2022Article
- Research Progress on Mono-ADP-Ribosyltransferases in Human Cell Biology.Frontiers in cell and developmental biology · 2022Review
- Active Peptide AR-9 FromFrontiers in pharmacology · 2022Article
- CE-MS for Proteomics and Intact Protein Analysis.Advances in experimental medicine and biology · 2021Article
- Human Long Noncoding RNA Interactome: Detection, Characterization and Function.International journal of molecular sciences · 2020Review
- An Advanced Strategy for Comprehensive Profiling of ADP-ribosylation Sites Using Mass Spectrometry-based Proteomics.Molecular & cellular proteomics : MCP · 2019Article
- Quantitation of Glycopeptides by ESI/MS - size of the peptide part strongly affects the relative proportions and allows discovery of new glycan compositions of Ceruloplasmin.Glycoconjugate journal · 2019Article
- Algorithms and design strategies towards automated glycoproteomics analysis.Mass spectrometry reviews · 2017Review
- De novo protein sequencing, humanization and in vitro effects of an antihuman CD34 mouse monoclonal antibody.Biochemistry and biophysics reports · 2017Article
- De Novo MS/MS Sequencing of Native Human Antibodies.Journal of proteome research · 2017Article
- Mass Spectrometric Immunoassays in Characterization of Clinically Significant Proteoforms.Proteomes · 2016Review
- The generating function approach for Peptide identification in spectral networks.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- Review
- PepExplorer: a similarity-driven tool for analyzing de novo sequencing results.Molecular & cellular proteomics : MCP · 2014Article
- Mass spectrometry-based analysis of glycoproteins and its clinical applications in cancer biomarker discovery.Clinical proteomics · 2014Article
- O-GlcNAc profiling: from proteins to proteomes.Clinical proteomics · 2014Article
- Expanding proteome coverage with orthogonal-specificity α-lytic proteases.Molecular & cellular proteomics : MCP · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The high-throughput nature of proteomics mass spectrometry is enabled by a productive combination of data acquisition protocols and the computational tools used to interpret the resulting spectra. One of the key components in mainstream protocols is the generation of tandem mass (MS/MS) spectra by peptide fragmentation using collision induced dissociation, the approach currently used in the large majority of proteomics experiments to routinely identify hundreds to thousands of proteins from single mass spectrometry runs. Complementary to these, alternative peptide fragmentation methods such as electron capture/transfer dissociation and higher-energy collision dissociation have consistently achieved significant improvements in the identification of certain classes of peptides, proteins, and post-translational modifications. Recognizing these advantages, mass spectrometry instruments now conveniently support fine-tuned methods that automatically alternate between peptide fragmentation modes for either different types of peptides or for acquisition of multiple MS/MS spectra from each peptide. But although these developments have the potential to substantially improve peptide identification, their routine application requires corresponding adjustments to the software tools and procedures used for automated downstream processing. This review discusses the computational implications of alternative and alternate modes of MS/MS peptide fragmentation and addresses some practical aspects of using such protocols for identification of peptides and post-translational modifications.
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Registered trials
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.