Paper Search Console

Home Search Page About Contact

Journal Title

Title of Journal: J Am Soc Mass Spectrom

Search In Journal Title:

Abbravation: Journal of The American Society for Mass Spectrometry

Search In Journal Abbravation:

Publisher

Springer US

Search In Publisher:

DOI

10.1016/j.amjmed.2012.12.003

Search In DOI:

ISSN

1879-1123

Search In ISSN:
Search In Title Of Papers:

CYCLONE—A Utility for Emphasis Type="BoldItalic"

Authors: Daniel Kavan Marek Kuzma Karel Lemr Kevin A Schug Vladimir Havlicek
Publish Date: 2013/05/24
Volume: 24, Issue: 8, Pages: 1177-1184
PDF Link

Abstract

We have developed a de novo sequencing software tool CYCLONE and applied it for determination of cyclic peptides The program uses a nonredundant 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 precharacterization to accomplish unambiguous bion series assignments Showcase examples were a cyclic tetradepsipeptide beauverolide a cyclic hexadepsipeptide roseotoxin A a lassolike 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 isotopecontaining data It can be downloaded from the http//msbiomedcascz/MSTools/ websiteThe authors acknowledge support for this work from the Ministry of Education Youth and Sports of the Czech Republic ME10013 IMIC institutional research concept RVO61388971 Charles University in Prague UNCE 204025/2012 and Czech Science Foundation P206/12/1150

Keywords:

References

.
Search In Abstract Of Papers:
Other Papers In This Journal:
  1. Distonic Ions: Editorial
  2. On the Efficiency of NHS Ester Cross-Linkers for Stabilizing Integral Membrane Protein Complexes
  3. Dynamic Interchanging Native States of Lymphotactin Examined by SNAPP-MS
  4. Quantitative Assessment of Protein Structural Models by Comparison of H/D Exchange MS Data with Exchange Behavior Accurately Predicted by DXCOREX
  5. Reflections on Charge State Distributions, Protein Structure, and the Mystical Mechanism of Electrospray Ionization
  6. Mass Spectrometry-Based Quantification of Pseudouridine in RNA
  7. Statistical Examination of the a and a + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions
  8. Perspective on Electrospray Ionization and Its Relation to Electrochemistry
  9. Untargeted Metabolomics Strategies—Challenges and Emerging Directions
  10. Development of a Magnetic Microbead Affinity Selection Screen (MagMASS) Using Mass Spectrometry for Ligands to the Retinoid X Receptor-α
  11. Structural Investigation of Protonated Azidothymidine and Protonated Dimer
  12. Application of Probe Electrospray Ionization Mass Spectrometry (PESI-MS) to Clinical Diagnosis: Solvent Effect on Lipid Analysis
  13. Ion-Molecule Clustering in Differential Mobility Spectrometry: Lessons Learned from Tetraalkylammonium Cations and their Isomers
  14. Charge Detection Mass Spectrometry for Single Ions with an Uncertainty in the Charge Measurement of 0.65 e
  15. Super-Atmospheric Pressure Electrospray Ion Source: Applied to Aqueous Solution
  16. Probing the Electron Capture Dissociation Mass Spectrometry of Phosphopeptides with Traveling Wave Ion Mobility Spectrometry and Molecular Dynamics Simulations
  17. Efficient Covalent Bond Formation in Gas-Phase Peptide–Peptide Ion Complexes with the Photoleucine Stapler
  18. Ion Trap Electric Field Characterization Using Slab Coupled Optical Fiber Sensors
  19. Picoelectrospray Ionization Mass Spectrometry Using Narrow-Bore Chemically Etched Emitters
  20. The H-Index of ‘An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database’
  21. Predicting Compensation Voltage for Singly-charged Ions in High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS)
  22. Native ESI Mass Spectrometry Can Help to Avoid Wrong Interpretations from Isothermal Titration Calorimetry in Difficult Situations
  23. Characterization of Tyrosine Nitration and Cysteine Nitrosylation Modifications by Metastable Atom-Activation Dissociation Mass Spectrometry
  24. Deconstructing Desorption Electrospray Ionization: Independent Optimization of Desorption and Ionization by Spray Desorption Collection
  25. Matrix Assisted Ionization in Vacuum, a Sensitive and Widely Applicable Ionization Method for Mass Spectrometry
  26. Localization of Post-Translational Modifications in Peptide Mixtures via High-Resolution Differential Ion Mobility Separations Followed by Electron Transfer Dissociation
  27. MALDI Mass Spectrometric Imaging of Lipids in Rat Brain Injury Models
  28. High Production of Small Organic Dicarboxylate Dianions by DESI and ESI
  29. Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data
  30. Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data
  31. Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms
Search Result: