ArticleJournal of the American Society for Mass Spectrometry2013
CYCLONE--a utility for de novo sequencing of microbial cyclic peptides.
Article in Journal of the American Society for Mass Spectrometry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed, 18 citations in OpenAlex.
- Affinity selection-mass spectrometry with linearizable macrocyclic peptide libraries.Science advances · 2025Article
- Genome mining strategies for ribosomally synthesised and post-translationally modified peptides.Computational and structural biotechnology journal · 2020Review
- Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides.Journal of the American Society for Mass Spectrometry · 2016Article
- Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks.Natural product reports · 2016Review
- Identification and Structural Characterization of Naturally-Occurring Broad-Spectrum Cyclic Antibiotics Isolated from Paenibacillus.Journal of the American Society for Mass Spectrometry · 2015Article
- CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra.Journal of the American Society for Mass Spectrometry · 2015Article
- Mass spectrometry of natural products: current, emerging and future technologies.Natural product reports · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed a de novo sequencing software tool (CYCLONE) and applied it for determination of cyclic peptides. The program uses a non-redundant database of 312 nonribosomal building blocks identified to date in bacteria and fungi (more than 230 additional residues in the database list were isobaric). The software was used to fully characterize the tandem mass spectrum of several cyclic peptides and provide sequence tags. The general strategy of the script was based on fragment ion pre-characterization to accomplish unambiguous b-ion series assignments. Showcase examples were a cyclic tetradepsipeptide beauverolide, a cyclic hexadepsipeptide roseotoxin A, a lasso-like hexapeptide pseudacyclin A, and a cyclic undecapeptide cyclosporin A. The extent of ion scrambling in smaller peptides was as low as 5 % of total ion current; this demonstrated the feasibility of CYCLONE de novo sequencing. The robustness of the script was also tested against database sets of various sizes and isotope-containing data. It can be downloaded from the http://ms.biomed.cas.cz/MSTools/ website. ᅟ
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.