PEAKS
algorithm · Graph / DP
PEAKS: algorithm · Graph / DP. Commercial DP-based de novo
Commercial DP-based de novo
| Kind | algorithm |
| Deep learning | no |
| Acquisition | DDA |
| Family | Graph / DP |
Papers describing it (7)
- An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum (2003, Lecture Notes in Computer Science, peer-reviewed)
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003, Rapid Communications in Mass Spectrometry, peer-reviewed)
- An effective algorithm for peptide de novo sequencing from MS/MS spectra (2005, Journal of Computer and System Sciences, peer-reviewed)
- Complexity and scoring function of MS/MS peptide de novo sequencing (2006, Computational Systems Bioinformatics, peer-reviewed)
- Improving de novo sequencing accuracy for Ion Trap data in PEAKS software (2007, presentation)
- Better score function for peptide identification with ETD MS/MS spectra (2010, BMC Bioinformatics, peer-reviewed)
- A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics (2022, Nature Communications, peer-reviewed)
Papers using it (140)
Applications and evaluations that ran this method. They are not counted among its authors below.
- An integrated De novo sequencing and virtual screening strategy for the discovery of low-abundance natural peptides with potential bioactivities from Asini Corii Colla (2026, Journal of Chromatography B, peer-reviewed)
- Sequence-resolved discovery and cellular validation of immunomodulatory peptides from cricket protein hydrolysate (2026, Future Foods, peer-reviewed)
- Ancient proteins identify various Denisovan remains from Southwest China (2026, Nature, peer-reviewed)
- Towards the establishment of a comprehensive food inspection system: An approach to utilize de novo peptide sequencing from MS/MS spectra (2026, Food and Humanity, peer-reviewed)
- Early maturation of host antimicrobial peptide defences is associated with host–pathogen coexistence (2026, Nature Chemical Biology, peer-reviewed)
- Sequence-Resolved Discovery of Immunomodulatory Peptides from Cricket Protein Hydrolysate as a Functional Alternative Protein Ingredient (2026, SSRN Electronic Journal, preprint)
- Enamel proteins from six Homo erectus specimens across China (2026, Nature, peer-reviewed)
- N-Terminal Coumarin Derivatization-Aided De Novo Peptide Sequencing and Its Application to Peptidomics Using LC-Trapped Ion Mobility Spectrometry-qTOF/MS (2026, Analytical Chemistry, peer-reviewed)
- Screening and Identification of TRPV1-Targeting Peptides from Apis mellifera Venom with Inflammatory Modulatory Potential (2026, Journal of Natural Products, peer-reviewed)
- N-terminal Coumarin Derivatization-aided De Novo Peptide Sequencing and its Application to Peptidomics using LC-trapped Ion Mobility Spectrometry-qTOF/MS (2026, ChemRxiv, preprint)
- Towards the establishment of a comprehensive food inspection system: an approach to utilise de novo peptide sequencing from MS/MS spectra (2026, SSRN Electronic Journal, preprint)
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2025, Cell Systems, peer-reviewed)
- Mass spectrometry-based analysis of rheumatoid factor (2025, Frontiers in Immunology, peer-reviewed)
- SequenceAssembler: A tool for protein sequence assembly from mass spectrometry data (2025, Journal of Proteomics, peer-reviewed)
- Expanding the repertoire of conopeptides from the venom of the vermivorous snail Conus regius (2025, Toxicon, peer-reviewed)
- The proteome of the late Middle Pleistocene Harbin individual (2025, Science, peer-reviewed)
- Structural Basis for Postfusion-Specific Binding to the Respiratory Syncytial Virus F Protein by the Canonical Antigenic Site I Antibody 131–2a (2025, ACS Infectious Diseases, peer-reviewed)
- Proteolytic signatures of coagulation identified by plasma peptidomics (2025, Journal of Thrombosis and Haemostasis, peer-reviewed)
- A green dichromophoric protein enabling foliage mimicry in arthropods (2025, Proceedings of the National Academy of Sciences, peer-reviewed)
- Enamel proteins reveal biological sex and genetic variability in southern African Paranthropus (2025, Science, peer-reviewed)
- Antidiabetic and Immunomodulatory Properties of Peptide Fractions from Sacha Inchi Oil Press-Cake (2025, Foods, peer-reviewed)
- Decoding Protein Glycosylation by an Integrative Mass Spectrometry-Based De Novo Sequencing Strategy (2025, JACS Au, peer-reviewed)
- Interferon-α promotes HLA-B-restricted presentation of conventional and alternative antigens in human pancreatic β-cells (2025, Nature Communications, peer-reviewed)
- SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells (2025, Frontiers in Immunology, peer-reviewed)
- Identification, screening, and comprehensive evaluation of novel thrombin inhibitory peptides from the hirudo produced using pepsin (2024, Frontiers in Pharmacology, peer-reviewed)
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2024, bioRxiv, preprint)
- Food processing drives the toxic lectin reduction and bioactive peptide enhancement in Pinellia ternata (2024, Current Research in Food Science, peer-reviewed)
- Proteomic Analysis of the Major Alkali-Soluble Inca Peanut (Plukenetia volubilis) Proteins (2024, Foods, peer-reviewed)
- Immunoglobulin repertoire sequencing and de novo sequencing – Powerful tools for identifying free light chains from patients with light chain cast nephropathy (2024, International Immunopharmacology, peer-reviewed)
- PeposX-Exhaust: A lightweight and efficient tool for identification of short peptides (2024, Food Chemistry: X, peer-reviewed)
- Improved detection of tryptic immunoglobulin variable region peptides by chromatographic and gas-phase fractionation techniques (2024, Cell Reports Methods, peer-reviewed)
- NovoLign: metaproteomics by sequence alignment (2024, bioRxiv, preprint)
- Olive Pomace Extract Contains Low Molecular Weight Peptides and Possesses ACE Inhibitory Activity (2024, International Journal of Molecular Sciences, peer-reviewed)
- Mirror-image trypsin digestion and sequencing of D-proteins (2024, Nature Chemistry, peer-reviewed)
- NovoLign: metaproteomics by sequence alignment (2024, ISME Communications, peer-reviewed)
- A novel metalloproteinase-derived cryptide from Bothrops cotiara venom inhibits angiotensin-converting enzyme activity (2024, Biochimie, peer-reviewed)
- Peposx-Exhaust: A Lightweight and Efficient Tool for Identification of Short Peptides (2023, SSRN Electronic Journal, preprint)
- Unveiling the peptidome diversity of Lachesis muta snake venom: Discovery of novel fragments of metalloproteinase, l-amino acid oxidase, and bradykinin potentiating peptides (2023, Biochemical and Biophysical Research Communications, peer-reviewed)
- Functional peptidomics analysis of Saccharomyces pastorianus protein hydrolysates based on different enzyme treatments (2023, Chinese Journal of Chromatography, peer-reviewed)
- Anti-methicillin-resistant Staphylococcus aureus and antibiofilm activity of new peptides produced by a Brevibacillus strain (2023, PeerJ, peer-reviewed)
- Direct Mass Spectrometry-Based Detection and Antibody Sequencing of Monoclonal Gammopathy of Undetermined Significance from Patient Serum: A Case Study (2023, Journal of Proteome Research, peer-reviewed)
- Characterization of natural peptides in Pheretima by integrating proteogenomics and label-free peptidomics (2023, Journal of Pharmaceutical Analysis, peer-reviewed)
- Exploring the Immunogenicity of Noncanonical HLA-I Tumor Ligands Identified through Proteogenomics (2023, Clinical Cancer Research, peer-reviewed)
- Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome (2023, Current Plant Biology, peer-reviewed)
- Next-Generation Sequencing for Venomics: Application of Multi-Enzymatic Limited Digestion for Inventorying the Snake Venom Arsenal (2023, Toxins, peer-reviewed)
- De novo sequencing of multiple tandem mass spectra of peptide containing SILAC labeling (2023, thesis)
- Isolated anti-Ro52 identifies a severe subset of Sjögren’s syndrome patients (2023, Frontiers in Immunology, peer-reviewed)
- Complementarity determining regions in SARS-CoV-2 hybrid immunity (2023, Frontiers in Immunology, peer-reviewed)
- HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search (2023, Journal of Proteome Research, peer-reviewed)
- Antibody sequences assembly method based on weighted de Bruijn graph (2023, Mathematical Biosciences and Engineering, peer-reviewed)
- Enrichment and fragmentation approaches for enhanced detection and characterization of endogenous glycosylated neuropeptides (2023, PROTEOMICS, peer-reviewed)
- Identification, Screening, and Comprehensive Evaluation of Novel DPP-IV Inhibitory Peptides from the Tilapia Skin Gelatin Hydrolysate Produced Using Ginger Protease (2022, Biomolecules, peer-reviewed)
- Venomics survey of six myrmicine ants provides insights into the molecular and structural diversity of their peptide toxins (2022, Insect Biochemistry and Molecular Biology, peer-reviewed)
- De novo assisted AFB1-Specific monoclonal antibody sequence assembly and comprehensive molecular characterization (2022, Analytical Biochemistry, peer-reviewed)
- Identification of Daboia siamensis venome using integrated multi-omics data (2022, Scientific Reports, peer-reviewed)
- Interaction With Fungi Promotes the Accumulation of Specific Defense Molecules in Orchid Tubers and May Increase the Value of Tubers for Biotechnological and Medicinal Applications: The Case Study of Interaction Between Dactylorhiza sp. and Tulasnella calospora (2022, Frontiers in Plant Science, peer-reviewed)
- Characterization of Proteasome-Generated Spliced Peptides Detected by Mass Spectrometry (2022, The Journal of Immunology, peer-reviewed)
- Meta-proteomic analysis of two mammoth’s trunks by EVA technology and high-resolution mass spectrometry for an indirect picture of their habitat and the characterization of the collagen type I, alpha-1 and alpha-2 sequence (2022, Amino Acids, peer-reviewed)
- Peptidomes and Structures Illustrate How SLA-I Micropolymorphism Influences the Preference of Binding Peptide Length (2022, Frontiers in Immunology, peer-reviewed)
- Characterisation of Endogenous Peptides Present in Virgin Olive Oil (2022, International Journal of Molecular Sciences, peer-reviewed)
- Identification of vicilin, legumin and antimicrobial peptide 2a as macadamia nut allergens (2022, Food Chemistry, peer-reviewed)
- Protein cycling in the eastern tropical North Pacific oxygen‐deficient zone: A de novo‐discovery peptidomic approach (2022, Limnology and Oceanography, peer-reviewed)
- Venomics and antivenomics of Indian spectacled cobra (Naja naja) from the Western Ghats (2022, Acta Tropica, peer-reviewed)
- Rapid de novo discovery of peptidomimetic affinity reagents for human angiotensin converting enzyme 2 (2022, Communications Chemistry, peer-reviewed)
- Mass spectrometry profiling and quantitation of changes in circulating hormones secreted over time in Cancer borealis hemolymph due to feeding behavior (2022, Analytical and Bioanalytical Chemistry, peer-reviewed)
- Protein Identification Strategies for the Greenshell Mussel Perna canaliculus (2021, thesis)
- Digging deeper into the immunopeptidome: characterization of post-translationally modified peptides presented by MHC I (2021, Journal of Proteins and Proteomics, peer-reviewed)
- Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma (2021, Molecular & Cellular Proteomics, peer-reviewed)
- Novel peptides contribute to the antimicrobial activity of camel milk fermented with Lactobacillus plantarum IS10 (2021, Food Control, peer-reviewed)
- The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires (2021, Molecular & Cellular Proteomics, peer-reviewed)
- Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and the snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered fatty acid accumulation via reallocation of carbon resources (2021, Biotechnology for Biofuels, peer-reviewed)
- Exploring the Sexual Dimorphism of Crustacean Neuropeptide Expression Using Callinectes sapidus as a Model Organism (2021, Journal of Proteome Research, peer-reviewed)
- Database-independent de novo metaproteomics of complex microbial communities (2021, Cell Systems, peer-reviewed)
- Enzymatic valorization process of yellow cocoon waste for production of antioxidative sericin and fibroin film (2021, Journal of Chemical Technology & Biotechnology, peer-reviewed)
- Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry (2021, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, peer-reviewed)
- Mass Spectrometry Quantification, Localization, and Discovery of Feeding-Related Neuropeptides in Cancer borealis (2021, ACS Chemical Neuroscience, peer-reviewed)
- Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking (2021, Journal of Proteomics, peer-reviewed)
- ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping (2020, Molecular & Cellular Proteomics, peer-reviewed)
- Rubisco activase requires residues in the large subunit N terminus to remodel inhibited plant Rubisco (2020, Journal of Biological Chemistry, peer-reviewed)
- Comparative gender peptidomics of Bothrops atrox venoms: are there differences between them? (2020, Journal of Venomous Animals and Toxins including Tropical Diseases, peer-reviewed)
- Resistant starch slows the progression of CKD in the 5/6 nephrectomy mouse model (2020, Physiological Reports, peer-reviewed)
- Elucidation of the Signatures of Proteasome-Catalyzed Peptide Splicing (2020, Frontiers in Immunology, peer-reviewed)
- Palaeoproteomics gives new insight into early southern African pastoralism (2020, Scientific Reports, peer-reviewed)
- Quantitative profiling of microbial communities by de novo metaproteomics (2020, bioRxiv, preprint)
- The shell matrix of the european thorny oyster, Spondylus gaederopus: microstructural and molecular characterization (2020, Journal of Structural Biology, peer-reviewed)
- Venom Peptide Repertoire of the European Myrmicine Ant Manica rubida: Identification of Insecticidal Toxins (2020, Journal of Proteome Research, peer-reviewed)
- Proteogenomic analysis of granulocyte macrophage colony- stimulating factor autoantibodies in the blood of a patient with autoimmune pulmonary alveolar proteinosis (2020, Scientific Reports, peer-reviewed)
- A Decomposition Based Multi-objective Genetic Programming Algorithm for Classification of Highly Imbalanced Tandem Mass Spectrometry (2020, Lecture Notes in Computer Science, peer-reviewed)
- Delineating the venom toxin arsenal of Malabar pit viper (Trimeresurus malabaricus) from the Western Ghats of India and evaluating its immunological cross-reactivity and in vitro cytotoxicity (2020, International Journal of Biological Macromolecules, peer-reviewed)
- Antihypertensive Effects of Virgin Olive Oil (Unfiltered) Low Molecular Weight Peptides with ACE Inhibitory Activity in Spontaneously Hypertensive Rats (2020, Nutrients, peer-reviewed)
- The Peptide Venom Composition of the Fierce Stinging Ant Tetraponera aethiops (Formicidae: Pseudomyrmecinae) (2019, Toxins, peer-reviewed)
- PepSAVI-MS Reveals a Proline-rich Antimicrobial Peptide in Amaranthus tricolor (2019, Journal of Natural Products, peer-reviewed)
- Preprocessing Tandem Mass Spectra Using Genetic Programming for Peptide Identification (2019, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- Learning to Rank Peptide-Spectrum Matches Using Genetic Programming (2019, 2019 IEEE Congress on Evolutionary Computation (CEC), peer-reviewed)
- ’Palaeoshellomics’ reveals the use of freshwater mother-of-pearl in prehistory (2019, eLife, peer-reviewed)
- TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets (2019, Nature Biotechnology, peer-reviewed)
- Math, science, history, unraveling the mystery—That all started with de novo! (2019, EuPA Open Proteomics, peer-reviewed)
- Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats (2019, PLOS ONE, peer-reviewed)
- Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome* (2018, Molecular & Cellular Proteomics, peer-reviewed)
- Deciphering the Molecular Diversity of an Ant Venom Peptidome through a Venomics Approach (2018, Journal of Proteome Research, peer-reviewed)
- A recombinant isoform of the Ole e 7 olive pollen allergen assembled by de novo mass spectrometry retains the allergenic ability of the natural allergen (2018, Journal of Proteomics, peer-reviewed)
- Mass spectrometry-assisted venom profiling of Hypnale hypnale found in the Western Ghats of India incorporating de novo sequencing approaches (2018, International Journal of Biological Macromolecules, peer-reviewed)
- Genetic Programming for Preprocessing Tandem Mass Spectra to Improve the Reliability of Peptide Identification (2018, 2018 IEEE Congress on Evolutionary Computation (CEC), peer-reviewed)
- Identification of <10 KD peptides in the water extraction of Venenum Bufonis from Bufo gargarizans using Nano LC-MS/MS and De novo sequencing (2018, Journal of Pharmaceutical and Biomedical Analysis, peer-reviewed)
- Evolutionary instability of CUG-Leu in the genetic code of budding yeasts (2018, Nature Communications, peer-reviewed)
- First report of the characterization of a snake venom apyrase (Ruviapyrase) from Indian Russell’s viper (Daboia russelii) venom (2018, International Journal of Biological Macromolecules, peer-reviewed)
- Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome (2018, bioRxiv, preprint)
- Disentangling thermal stress responses in a reef-calcifier and its photosymbionts by shotgun proteomics (2018, Scientific Reports, peer-reviewed)
- Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries (2017, ACS Combinatorial Science, peer-reviewed)
- The sequence coverage in different methods of mass spectrometry data analysis obtained on model proteins (2017, Biomeditsinskaya Khimiya, peer-reviewed)
- Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus (2017, Open Biology, peer-reviewed)
- Analysis of skin derived peptides from the Cuyaba Dwarf Frog Physalaemus nattereri by off-line LC MALDI MS/MS (2017, International Journal of Mass Spectrometry, peer-reviewed)
- Discovery of Novel Antimicrobial Peptides from Varanus komodoensis (Komodo Dragon) by Large-Scale Analyses and De-Novo-Assisted Sequencing Using Electron-Transfer Dissociation Mass Spectrometry (2017, Journal of Proteome Research, peer-reviewed)
- Characterisation of urinary WFDC12 in small nocturnal basal primates, mouse lemurs (Microcebus spp.) (2017, Scientific Reports, peer-reviewed)
- Peptidomics of Acanthoscurria gomesiana spider venom reveals new toxins with potential antimicrobial activity (2017, Journal of Proteomics, peer-reviewed)
- Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome (2016, PROTEOMICS, peer-reviewed)
- Revealing the functional structure of a new PLA2 K49 from Bothriopsis taeniata snake venom employing automatic “de novo” sequencing using CID/HCD/ETD MS/MS analyses (2015, Journal of Proteomics, peer-reviewed)
- Large Scale Discovery and De Novo-Assisted Sequencing of Cationic Antimicrobial Peptides (CAMPs) by Microparticle Capture and Electron-Transfer Dissociation (ETD) Mass Spectrometry (2015, Journal of Proteome Research, peer-reviewed)
- De novo sequencing of disulphide rich peptides using tandem mass spectrometry (2015, thesis)
- Novel Antifungal Peptides Produced by Leuconostoc mesenteroides DU15 Effectively Inhibit Growth of Aspergillus niger (2015, Journal of Food Science, peer-reviewed)
- Antiproliferative effect of Dendrobium catenatum Lindley polypeptides against human liver, gastric and breast cancer cell lines (2015, Food & Function, peer-reviewed)
- PepExplorer: A Similarity-driven Tool for Analyzing de Novo Sequencing Results (2014, Molecular & Cellular Proteomics, peer-reviewed)
- Practical Ring-Opening Strategy for the Sequence Determination of Cyclic Peptides from One-Bead-One-Compound Libraries (2013, ACS Combinatorial Science, peer-reviewed)
- Moving Pieces in a Venomic Puzzle: Unveiling Post-translationally Modified Toxins from Tityus serrulatus (2013, Journal of Proteome Research, peer-reviewed)
- Integrating de novo Sequencing and Database Search for Monoclonal Antibody Sequencing (2013, Europe PMC (PubMed Central), abstract)
- Proteomic studies highlight outer‐membrane proteins related to biofilm development in the marine bacterium Pseudoalteromonas sp. D41 (2012, PROTEOMICS, peer-reviewed)
- Partial De Novo Sequencing and Unusual CID Fragmentation of a 7 kDa, Disulfide-Bridged Toxin (2012, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- Introducing an Asp-Pro Linker in the Synthesis of Random One-Bead-One-Compound Hexapeptide Libraries Compatible with ESI-MS Analysis (2012, ACS Combinatorial Science, peer-reviewed)
- Extensive Characterization of Tupaia belangeri Neuropeptidome Using an Integrated Mass Spectrometric Approach (2012, Journal of Proteome Research, peer-reviewed)
- Isolation and determination of the primary structure of a lectin protein from the serum of the American alligator (Alligator mississippiensis) (2012, Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, peer-reviewed)
- Integrating de Novo Sequencing and Database Search for Peptide Identification (2012, Europe PMC (PubMed Central), abstract)
- Extensive De Novo Sequencing of New Parvalbumin Isoforms Using a Novel Combination of Bottom-Up Proteomics, Accurate Molecular Mass Measurement by FTICR−MS, and Selected MS/MS Ion Monitoring (2010, Journal of Proteome Research, peer-reviewed)
- Immune Responses Are Characterized by Specific Shared Immunoglobulin Peptides That Can Be Detected by Proteomic Techniques (2010, Journal of Biological Chemistry, peer-reviewed)
- Plant‐extract‐induced changes in the proteome of the soil‐borne pathogenic fungus Thielaviopsis basicola (2010, PROTEOMICS, peer-reviewed)
- De Novo Interpretation of Tandem Mass Spectra (2009, Current Protocols in Bioinformatics, peer-reviewed)
- A comparative study of the accuracy of several de novo sequencing software packages for datasets derived by matrix‐assisted laser desorption/ionisation and electrospray (2008, Rapid Communications in Mass Spectrometry, peer-reviewed)
- A proteomic‐based approach for the characterization of some major structural proteins involved in host–parasite relationships from the silkworm parasite Nosema bombycis (Microsporidia) (2007, PROTEOMICS, peer-reviewed)
- De novo protein sequence analysis of Macaca mulatta (2007, BMC Genomics, peer-reviewed)
- Molecular Diversity in Venom from the Australian Brown Snake, Pseudonaja textilis (2006, Molecular & Cellular Proteomics, peer-reviewed)
- Defining parameters for homology-tolerant database searching (2004, PubMed, peer-reviewed)