ArticleJournal of the American Society for Mass Spectrometry2015
CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra.
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 15 papers.
What it found
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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.
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Who cites it
15 citing papers in PubMed.
- Annotation and Dereplication of Peptidic Natural Products (PNPs).Methods in molecular biology (Clifton, N.J.) · 2027Article
- Affinity selection-mass spectrometry with linearizable macrocyclic peptide libraries.Science advances · 2025Article
- Exploring the Siderophore Portfolio for Mass Spectrometry-Based Diagnosis of Scedosporiosis and Lomentosporiosis.ACS omega · 2024Article
- Exploring the Effects of Cyclosporin A to Isocyclosporin A Rearrangement on Ion Mobility Separation.Analytical chemistry · 2024Article
- Review
- The use of nitrogen-15 in microbial natural product discovery and biosynthetic characterization.Frontiers in microbiology · 2023Review
- Identification of Novel Microcystins Using High-Resolution MS and MSEnvironmental science & technology · 2022Article
- MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis.Journal of cheminformatics · 2021Article
- Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain.The protein journal · 2020Article
- Metabolic profiling of Fusarium oxysporum f. sp. conglutinans race 2 in dual cultures with biocontrol agents Bacillus amyloliquefaciens, Pseudomonas aeruginosa, and Trichoderma harzianum.Folia microbiologica · 2019Article
- Gold(I) Cationization Promotes Ring Opening in Lysine-Containing Cyclic Peptides.Journal of the American Society for Mass Spectrometry · 2019Article
- Software solutions for evaluation and visualization of laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI) data: a short overview.Journal of cheminformatics · 2019Review
- Membrane depolarization and aberrant lipid distributions in the neonatal rat brain following hypoxic-ischaemic insult.Scientific reports · 2018Article
- Non-invasive and invasive diagnoses of aspergillosis in a rat model by mass spectrometry.Scientific reports · 2017Article
- Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides.Journal of the American Society for Mass Spectrometry · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nonribosomal peptides have a wide range of biological and medical applications. Their identification by tandem mass spectrometry remains a challenging task. A new open-source de novo peptide identification engine CycloBranch was developed and successfully applied in identification or detailed characterization of 11 linear, cyclic, branched, and branch-cyclic peptides. CycloBranch is based on annotated building block databases the size of which is defined by the user according to ribosomal or nonribosomal peptide origin. The current number of involved nonisobaric and isobaric building blocks is 287 and 521, respectively. Contrary to all other peptide sequencing tools utilizing either peptide libraries or peptide fragment libraries, CycloBranch represents a true de novo sequencing engine developed for accurate mass spectrometric data. It is a stand-alone and cross-platform application with a graphical and user-friendly interface; it supports mzML, mzXML, mgf, txt, and baf file formats and can be run in parallel on multiple threads. It can be downloaded for free from http://ms.biomed.cas.cz/cyclobranch/ , where the User's manual and video tutorials can be found.
Indexed as
Identifiers
26195308What 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.