ArticleJournal of the American Society for Mass Spectrometry2015
Novor: real-time peptide de novo sequencing software.
Article in Journal of the American Society for Mass Spectrometry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers.
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107 citing papers in PubMed.
- Artificial Intelligence and Machine Learning in Mass Spectrometry-Based Proteomics and Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Integrated Genome Mining and Bioactivity-Guided Isolation of Antimicrobial Peptides from Bacillus amyloliquefaciens BS4.Probiotics and antimicrobial proteins · 2026Article
- Mass Spectrometry-Based De Novo Sequencing of N-Glycosylated Light Chains: Linking Urinary Proteoforms to In Situ Renal Amyloid Deposits.Molecular & cellular proteomics : MCP · 2026Article
- MARLOWE: taxonomic characterization of unknown samples for forensics using de novo peptide identification.Scientific reports · 2026Article
- Proteomic analysis of dental enamel from 20 Homo naledi individuals shows no male markers.Cell · 2026Article
- A Viral Mutation Profiling and Discovery Strategy for Sensitive Multiplex Detection of Viruses and Variants in Saliva by Proteomics.bioRxiv : the preprint server for biology · 2026Article
- MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing.Bioinformatics (Oxford, England) · 2026Article
- Discovery of Iron-Chelating Peptides fromFoods (Basel, Switzerland) · 2026Article
- Identification of non-canonical peptides with moPepGen.Nature biotechnology · 2026Article
- DiNovo enables high-coverage and high-confidence de novo peptide sequencing via mirror proteases and deep learning.Nature communications · 2026Article
- Automatic Selection of Search Parameter Values for Mass Spectrometry-Based Search Engines.Journal of proteome research · 2026Article
- Mass Spectrometry-Based Validation of Chimeric RNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics.Analytical chemistry · 2025Article
- Article
- DigDig: A Software for In-Depth Analysis and Comparison of Proteolytic Digestion.Analytical chemistry · 2025Article
- Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins.Molecular biology and evolution · 2025Article
- Proteomic Insights into Bacterial Responses to Antibiotics: A Narrative Review.International journal of molecular sciences · 2025Review
- Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases.Nature communications · 2025Article
- Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra.Journal of proteome research · 2025Article
47 more citing papers are in PubMed but not listed here.
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Authors and funding
1 author.
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Abstract
De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today's peptide de novo sequencing analyses. To improve the accuracy, Novor's scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today's mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data. Graphical Abstract ᅟ.
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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.