ReviewProtein science : a publication of the Protein Society2020
Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification.
Review in Protein science : a publication of the Protein Society, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- MARLOWE: taxonomic characterization of unknown samples for forensics using de novo peptide identification.Scientific reports · 2026Article
- Optimization of the Quantum-Si Platinum Single-Molecule Protein Sequencing Platform Toward Improved Complex-Matrix Protein Identification.ACS omega · 2026Article
- De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.Environmental microbiome · 2025Article
- A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.mSphere · 2024Article
- Review
- The Research Progress of Bioactive Peptides Derived from Traditional Natural Products in China.Molecules (Basel, Switzerland) · 2023Review
- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly.Briefings in bioinformatics · 2023Article
- Finding haplotypic signatures in proteins.GigaScience · 2022Article
- Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern.Journal of proteome research · 2022Article
- Considerations for constructing a protein sequence database for metaproteomics.Computational and structural biotechnology journal · 2022Review
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification.Protein science : a publication of the Protein Society · 2020Review
Corrections and comments
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Authors and funding
3 authors.
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Abstract
Mass spectrometry-based proteomics is a popular and powerful method for precise and highly multiplexed protein identification. The most common method of analyzing untargeted proteomics data is called database searching, where the database is simply a collection of protein sequences from the target organism, derived from genome sequencing. Experimental peptide tandem mass spectra are compared to simplified models of theoretical spectra calculated from the translated genomic sequences. However, in several interesting application areas, such as forensics, archaeology, venomics, and others, a genome sequence may not be available, or the correct genome sequence to use is not known. In these cases, de novo peptide identification can play an important role. De novo methods infer peptide sequence directly from the tandem mass spectrum without reference to a sequence database, usually using graph-based or machine learning algorithms. In this review, we provide a basic overview of de novo peptide identification methods and applications, briefly covering de novo algorithms and tools, and focusing in more depth on recent applications from venomics, metaproteomics, forensics, and characterization of antibody drugs.
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