ArticleBioinformatics (Oxford, England)2013
UniNovo: a universal tool for de novo peptide sequencing.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed.
- High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Developing Well-Annotated Species-Specific Protein Databases Using Comparative Proteogenomics: An Update.Advances in experimental medicine and biology · 2026Review
- Article
- De Novo Sequencing of Peptides from Tandem Mass Spectra and Applications in Proteogenomics.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A Shotgun Proteomic-Based Approach with a Q-Exactive Hybrid Quadrupole-Orbitrap High-Resolution Mass Spectrometer for the Assessment of Pesticide Mixture-Induced Neurotoxicity on a 3D-Developed Neurospheroid Model from Human Brain Meningiomas: Identification of Trityl-Post-Translational Modification.Journal of proteome research · 2024Article
- Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity.Nature communications · 2024Article
- Proteomics techniques in protein biomarker discovery.Quantitative biology (Beijing, China) · 2024Review
- Accurate de novo peptide sequencing using fully convolutional neural networks.Nature communications · 2023Article
- Shotgun Proteomic-Based Approach with a Q-Exactive Hybrid Quadrupole-Orbitrap High-Resolution Mass Spectrometer for Protein Adductomics on a 3D Human Brain Tumor Neurospheroid Culture Model: The Identification of Adduct Formation in Calmodulin-Dependent Protein Kinase-2 and Annexin-A1 Induced by Pesticide Mixture.Journal of proteome research · 2023Article
- Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.FEMS microbiology reviews · 2023Review
- Recent advances in mass spectrometry analysis of neuropeptides.Mass spectrometry reviews · 2023Review
- Peptidomics Methods Applied to the Study of Flower Development.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The Current State-of-the-Art Identification of Unknown Proteins Using Mass Spectrometry Exemplified on De Novo Sequencing of a Venom Protease fromMolecules (Basel, Switzerland) · 2022Review
- Software Options for the Analysis of MS-Proteomic Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Omics-Driven Biotechnology for Industrial Applications.Frontiers in bioengineering and biotechnology · 2021Review
- Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives.International journal of molecular sciences · 2020Review
- A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of this Field.Proteomes · 2020Review
- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.International journal of molecular sciences · 2020Review
- Metaproteomics of the human gut microbiota: Challenges and contributions to other OMICS.Clinical mass spectrometry (Del Mar, Calif.) · 2019Review
- MCtandem: an efficient tool for large-scale peptide identification on many integrated core (MIC) architecture.BMC bioinformatics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
motivationMass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but de novo peptide sequencing algorithms to analyze tandem mass (MS/MS) spectra are lagging behind. Although existing de novo sequencing tools perform well on certain types of spectra [e.g. Collision Induced Dissociation (CID) spectra of tryptic peptides], their performance often deteriorates on other types of spectra, such as Electron Transfer Dissociation (ETD), Higher-energy Collisional Dissociation (HCD) spectra or spectra of non-tryptic digests. Thus, rather than developing a new algorithm for each type of spectra, we develop a universal de novo sequencing algorithm called UniNovo that works well for all types of spectra or even for spectral pairs (e.g. CID/ETD spectral pairs). UniNovo uses an improved scoring function that captures the dependences between different ion types, where such dependencies are learned automatically using a modified offset frequency function.
resultsThe performance of UniNovo is compared with PepNovo+, PEAKS and pNovo using various types of spectra. The results show that the performance of UniNovo is superior to other tools for ETD spectra and superior or comparable with others for CID and HCD spectra. UniNovo also estimates the probability that each reported reconstruction is correct, using simple statistics that are readily obtained from a small training dataset. We demonstrate that the estimation is accurate for all tested types of spectra (including CID, HCD, ETD, CID/ETD and HCD/ETD spectra of trypsin, LysC or AspN digested peptides). AVAILABILITY: UniNovo is implemented in JAVA and tested on Windows, Ubuntu and OS X machines. UniNovo is available at http://proteomics.ucsd.edu/Software/UniNovo.html along with the manual.
Indexed as
Identifiers
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.