ReviewMass spectrometry reviews
Lessons in de novo peptide sequencing by tandem mass spectrometry.
Review in Mass spectrometry reviews. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
80 citing papers in PubMed.
- Understanding Mass Spectrometry: From Ion Generation to Spectral Interpretation.Journal of mass spectrometry : JMS · 2026Article
- Revealing deamidation and isoaspartate formation during peptide analysis, purification and storage by tandem mass spectrometry.RSC medicinal chemistry · 2026Article
- Modanovo: A Unified Model for Post-translational Modification-Aware De Novo Sequencing Using Experimental Spectra From In Vivo and Synthetic Peptides.Molecular & cellular proteomics : MCP · 2026Article
- Peptidomics-based identification of endogenous free peptides fromFrontiers in pharmacology · 2026Article
- Artificial Intelligence and the Evolving Landscape of Immunopeptidomics.Proteomics. Clinical applications · 2025Review
- The Identification and Analysis of Novel Umami Peptides in Lager Beer and Their Multidimensional Effects on the Sensory Attributes of the Beer Body.Foods (Basel, Switzerland) · 2025Article
- Composite Mapping for Peptide-Based Data Storage with Higher Coding Density and Fewer Synthesis Cycles.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Crucian Carp-Derived ACE-Inhibitory Peptides with In Vivo Antihypertensive Activity: Insights into Bioactivity, Mechanism, and Safety.Molecules (Basel, Switzerland) · 2025Article
- Prime mass amino acids: A new numbers based classification of significance to mass spectrometry and protein biology.European journal of mass spectrometry (Chichester, England) · 2025Article
- Bovine Milk Protein-Derived Preparations and Their Hydrolysates as Sources of ACE-Inhibitory, DPP-IV-Inhibitory, and Antioxidative Peptides Analyzed Using in Silico and in Vitro Protocols.International journal of molecular sciences · 2025Article
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments.Nature machine intelligence · 2025Article
- Novel Insights into the Nobilamide Family from a Deep-SeaMarine drugs · 2025Article
- Optimized and Robust Workflow for Quantifying the Canonical Histone Ubiquitination Marks H2AK119ub and H2BK120ub by LC-MS/MS.Journal of proteome research · 2024Article
- The Hunt Lab Guide to De Novo Peptide Sequence Analysis by Tandem Mass Spectrometry.Molecular & cellular proteomics : MCP · 2024Article
- A generalized protein identification method for novel and diverse sequencing technologies.NAR genomics and bioinformatics · 2024Article
- Sequencing of Phosphopeptides Using a Sequential Charge Inversion Ion/Ion Reaction and Electron Capture Dissociation Workflow.Journal of the American Society for Mass Spectrometry · 2024Article
- An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS.bioRxiv : the preprint server for biology · 2024Article
- A Protocol to Depict the Proteolytic Processes Using a Combination of Metal-Organic Materials (MOMs), Electron Paramagnetic Resonance (EPR), and Mass Spectrometry (MS).Bio-protocol · 2024Article
- Mass Spectrometric De Novo Sequencing of Natural Peptides.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Origins, Technological Advancement, and Applications of Peptidomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Mass spectrometry has become the method of choice for the qualitative and quantitative characterization of protein mixtures isolated from all kinds of living organisms. The raw data in these studies are MS/MS spectra, usually of peptides produced by proteolytic digestion of a protein. These spectra are "translated" into peptide sequences, normally with the help of various search engines. Data acquisition and interpretation have both been automated, and most researchers look only at the summary of the identifications without ever viewing the underlying raw data used for assignments. Automated analysis of data is essential due to the volume produced. However, being familiar with the finer intricacies of peptide fragmentation processes, and experiencing the difficulties of manual data interpretation allow a researcher to be able to more critically evaluate key results, particularly because there are many known rules of peptide fragmentation that are not incorporated into search engine scoring. Since the most commonly used MS/MS activation method is collision-induced dissociation (CID), in this article we present a brief review of the history of peptide CID analysis. Next, we provide a detailed tutorial on how to determine peptide sequences from CID data. Although the focus of the tutorial is de novo sequencing, the lessons learned and resources supplied are useful for data interpretation in general.
Indexed as
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What OpenQuestion holds
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.