Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

You’ve supercharged your research process with ACS and Mendeley!

STEP 1:
Click to create an ACS ID

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

MENDELEY PAIRING EXPIRED
Your Mendeley pairing has expired. Please reconnect
ACS Publications. Most Trusted. Most Cited. Most Read
CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra
My Activity

Figure 1Loading Img
    Research Article

    CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra
    Click to copy article linkArticle link copied!

    • Jiří Novák
      Jiří Novák
      Institute of Microbiology ASCR, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech Republic
    • Karel Lemr
      Karel Lemr
      Institute of Microbiology ASCR, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech Republic
      Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
      More by Karel Lemr
    • Kevin A. Schug
      Kevin A. Schug
      Department of Chemistry and Biochemistry, The University of Texas at Arlington, 76019-0065, Arlington, TX, USA
    • Vladimír Havlíček
      Vladimír Havlíček
      Institute of Microbiology ASCR, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech Republic
      Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
    Other Access OptionsSupporting Information (1)

    Journal of The American Society for Mass Spectrometry

    Cite this: J. Am. Soc. Mass Spectrom. 2015, 26, 10, 1780–1786
    Click to copy citationCitation copied!
    https://doi.org/10.1007/s13361-015-1211-1
    Published July 21, 2015
    Copyright © 2015 © American Society for Mass Spectrometry 2015

    Abstract

    Click to copy section linkSection link copied!
    Abstract Image

    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.

    Copyright © 2015 © American Society for Mass Spectrometry 2015

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. Add or change your institution or let them know you’d like them to include access.

    Supporting Information

    Click to copy section linkSection link copied!

    Terms & Conditions

    Electronic Supporting Information files are available without a subscription to ACS Web Editions. The American Chemical Society holds a copyright ownership interest in any copyrightable Supporting Information. Files available from the ACS website may be downloaded for personal use only. Users are not otherwise permitted to reproduce, republish, redistribute, or sell any Supporting Information from the ACS website, either in whole or in part, in either machine-readable form or any other form without permission from the American Chemical Society. For permission to reproduce, republish and redistribute this material, requesters must process their own requests via the RightsLink permission system. Information about how to use the RightsLink permission system can be found at http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    Click to copy section linkSection link copied!

    This article is cited by 34 publications.

    1. Hynek Mácha, Jakub Zápal, Marek Kuzma, Dominika Luptáková, Karel Lemr, Vladimír Havlíček. Exploring the Effects of Cyclosporin A to Isocyclosporin A Rearrangement on Ion Mobility Separation. Analytical Chemistry 2024, 96 (10) , 4163-4170. https://doi.org/10.1021/acs.analchem.3c05165
    2. Jiahao Wan, Marianna Nytka, Haocheng Qian, Kim Vu, Karel Lemr, František Tureček. Nitrile Imines as Peptide and Oligonucleotide Photo-Cross-Linkers in Gas-Phase Ions. Journal of the American Society for Mass Spectrometry 2024, 35 (2) , 344-356. https://doi.org/10.1021/jasms.3c00379
    3. Hongyi Zhu, Václav Zima, Emily R. Ding, František Tureček. Carbene Cross-Linking in Gas-Phase Peptide Ion Scaffolds. Journal of the American Society for Mass Spectrometry 2023, 34 (4) , 763-774. https://doi.org/10.1021/jasms.3c00023
    4. David Baliu-Rodriguez, Nicholas J. Peraino, Sanduni H. Premathilaka, Johnna A. Birbeck, Tomás Baliu-Rodriguez, Judy A. Westrick, Dragan Isailovic. Identification of Novel Microcystins Using High-Resolution MS and MSn with Python Code. Environmental Science & Technology 2022, 56 (3) , 1652-1663. https://doi.org/10.1021/acs.est.1c04296
    5. Emma Ricart, Maude Pupin, Markus Müller, Frédérique Lisacek. Automatic Annotation and Dereplication of Tandem Mass Spectra of Peptidic Natural Products. Analytical Chemistry 2020, 92 (24) , 15862-15871. https://doi.org/10.1021/acs.analchem.0c03208
    6. Jiří Novák, Anton Škríba, Vladimír Havlíček. CycloBranch 2: Molecular Formula Annotations Applied to imzML Data Sets in Bimodal Fusion and LC-MS Data Files. Analytical Chemistry 2020, 92 (10) , 6844-6849. https://doi.org/10.1021/acs.analchem.0c00170
    7. David J. Foreman, John T. Lawler, Mary L. Niedrauer, Matthew A. Hostetler, Scott A. McLuckey. Gold(I) Cationization Promotes Ring Opening in Lysine-Containing Cyclic Peptides. Journal of the American Society for Mass Spectrometry 2019, 30 (10) , 1914-1922. https://doi.org/10.1007/s13361-019-02247-x
    8. Jakub Přichystal, Kevin A. Schug, Karel Lemr, Jiří Novák, and Vladimír Havlíček . Structural Analysis of Natural Products. Analytical Chemistry 2016, 88 (21) , 10338-10346. https://doi.org/10.1021/acs.analchem.6b02386
    9. Christopher M. Crittenden, W. Ryan Parker, Zachary B. Jenner, Kerry A. Bruns, Lucas D. Akin, William M. McGee, Eugene Ciccimaro, Jennifer S. Brodbelt. Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides. Journal of the American Society for Mass Spectrometry 2016, 27 (5) , 856-863. https://doi.org/10.1007/s13361-016-1355-7
    10. František Tureček. Covalent crosslinking in gas-phase biomolecular ions. An account and perspective. Physical Chemistry Chemical Physics 2023, 25 (47) , 32292-32304. https://doi.org/10.1039/D3CP04879A
    11. Anuj Ranjan, Vishnu D. Rajput, Evgeniya Valeryevna Prazdnova, Manisha Gurnani, Pallavi Bhardwaj, Shikha Sharma, Svetlana Sushkova, Saglara S. Mandzhieva, Tatiana Minkina, Jebi Sudan, Sajad Majeed Zargar, Abhishek Chauhan, Tanu Jindal. Nature’s Antimicrobial Arsenal: Non-Ribosomal Peptides from PGPB for Plant Pathogen Biocontrol. Fermentation 2023, 9 (7) , 597. https://doi.org/10.3390/fermentation9070597
    12. Kalindi D. Morgan. The use of nitrogen-15 in microbial natural product discovery and biosynthetic characterization. Frontiers in Microbiology 2023, 14 https://doi.org/10.3389/fmicb.2023.1174591
    13. Susana P. Gaudêncio, Engin Bayram, Lada Lukić Bilela, Mercedes Cueto, Ana R. Díaz-Marrero, Berat Z. Haznedaroglu, Carlos Jimenez, Manolis Mandalakis, Florbela Pereira, Fernando Reyes, Deniz Tasdemir. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Marine Drugs 2023, 21 (5) , 308. https://doi.org/10.3390/md21050308
    14. Jiří Novák, Kevin A Schug, Vladimír Havlíček. Quantitation of small molecules from liquid chromatography—mass spectrometric accurate mass datasets using CycloBranch. European Journal of Mass Spectrometry 2023, 29 (2) , 102-110. https://doi.org/10.1177/14690667231164766
    15. Jan Přívratský, Jiří Novák. MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis. Journal of Cheminformatics 2021, 13 (1) https://doi.org/10.1186/s13321-021-00530-2
    16. Cláudia Covas, Beatriz Almeida, Ana Cristina Esteves, Joana Lourenço, Pedro Domingues, Tânia Caetano, Sónia Mendo. Peptone from casein, an antagonist of nonribosomal peptide synthesis: a case study of pedopeptins produced by Pedobacter lusitanus NL19. New Biotechnology 2021, 60 , 62-71. https://doi.org/10.1016/j.nbt.2020.07.006
    17. Anna S. Pavlova, Georgii D. Ozhegov, Georgij P. Arapidi, Ivan O. Butenko, Eduard S. Fomin, Nikolai A. Alemasov, Dmitry A. Afonnikov, Dina R. Yarullina, Vadim T. Ivanov, Vadim M. Govorun, Airat R. Kayumov. Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain. The Protein Journal 2020, 39 (1) , 73-84. https://doi.org/10.1007/s10930-019-09879-8
    18. Ralf Weiskirchen, Sabine Weiskirchen, Philipp Kim, Robert Winkler. 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 2019, 11 (1) https://doi.org/10.1186/s13321-019-0338-7
    19. Andrea Palyzová, Kateřina Svobodová, Lucie Sokolová, Jiří Novák, Čeněk Novotný. 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 2019, 64 (6) , 779-787. https://doi.org/10.1007/s12223-019-00690-7
    20. Claudia Nelson, Raymond Bacala, Baylie Gigolyk, Evelyn Ang, Haley Neustaeter, Emy Komatsu, Oleg Krokhin, Dave Hatcher, Hélène Perreault. Characterization of Whole and Fragmented Wild-Type Porcine IgG. 2019https://doi.org/10.5772/intechopen.82792
    21. Tomas Pluhacek, Anton Skriba, Jiri Novak, Dominika Luptakova, Vladimir Havlicek. Analysis of Microbial Siderophores by Mass Spectrometry. 2019, 131-153. https://doi.org/10.1007/978-1-4939-9488-5_12
    22. Jameel R. Al-Obaidi. Proteoinformatics and Agricultural Biotechnology Research: Applications and Challenges. 2019, 1-27. https://doi.org/10.1007/978-3-030-19318-8_1
    23. Dominika Luptakova, Ladislav Baciak, Tomas Pluhacek, Anton Skriba, Blanka Sediva, Vladimir Havlicek, Ivo Juranek. Membrane depolarization and aberrant lipid distributions in the neonatal rat brain following hypoxic-ischaemic insult. Scientific Reports 2018, 8 (1) https://doi.org/10.1038/s41598-018-25088-2
    24. Jiří Novák, Anton Škríba, Jakub Zápal, Marek Kuzma, Vladimír Havlíček. CycloBranch: An open tool for fine isotope structures in conventional and product ion mass spectra. Journal of Mass Spectrometry 2018, 53 (11) , 1097-1103. https://doi.org/10.1002/jms.4285
    25. Andoni Ramirez-Garcia, Aize Pellon, Aitor Rementeria, Idoia Buldain, Eliana Barreto-Bergter, Rodrigo Rollin-Pinheiro, Jardel Vieira de Meirelles, Mariana Ingrid D S Xisto, Stephane Ranque, Vladimir Havlicek, Patrick Vandeputte, Yohann Le Govic, Jean-Philippe Bouchara, Sandrine Giraud, Sharon Chen, Johannes Rainer, Ana Alastruey-Izquierdo, Maria Teresa Martin-Gomez, Leyre M López-Soria, Javier Peman, Carsten Schwarz, Anne Bernhardt, Kathrin Tintelnot, Javier Capilla, Adela Martin-Vicente, Jose Cano-Lira, Markus Nagl, Michaela Lackner, Laszlo Irinyi, Wieland Meyer, Sybren de Hoog, Fernando L Hernando. Scedosporium and Lomentospora: an updated overview of underrated opportunists. Medical Mycology 2018, 56 (suppl_1) , S102-S125. https://doi.org/10.1093/mmy/myx113
    26. Chad Townsend, Akihiro Furukawa, Joshua Schwochert, Cameron R. Pye, Quinn Edmondson, R. Scott Lokey. CycLS: Accurate, whole-library sequencing of cyclic peptides using tandem mass spectrometry. Bioorganic & Medicinal Chemistry 2018, 26 (6) , 1232-1238. https://doi.org/10.1016/j.bmc.2018.01.027
    27. Anton Skriba, Vladimir Havlicek. Mass spectrometry imaging of illicit drugs in latent fingerprints by matrix-free and matrix-assisted desorption/ionization techniques. European Journal of Mass Spectrometry 2018, 24 (1) , 124-128. https://doi.org/10.1177/1469066717728007
    28. Anjana Rustagi, Garvita Singh, Shachi Agrawal, Prem Kumar Gupta. Proteomic Studies Revealing Enigma of Plant–Pathogen Interaction. 2018, 239-264. https://doi.org/10.1007/978-981-10-7371-7_11
    29. Dominika Luptáková, Tomáš Pluháček, Miloš Petřík, Jiří Novák, Andrea Palyzová, Lucie Sokolová, Anton Škríba, Blanka Šedivá, Karel Lemr, Vladimír Havlíček. Non-invasive and invasive diagnoses of aspergillosis in a rat model by mass spectrometry. Scientific Reports 2017, 7 (1) https://doi.org/10.1038/s41598-017-16648-z
    30. Jiří Novák, Lucie Sokolová, Karel Lemr, Tomáš Pluháček, Andrea Palyzová, Vladimír Havlíček. Batch-processing of imaging or liquid-chromatography mass spectrometry datasets and De Novo sequencing of polyketide siderophores. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2017, 1865 (7) , 768-775. https://doi.org/10.1016/j.bbapap.2016.12.003
    31. Sujata Baral, Swakkhar Shatabda, Mahmood A Rashid. CycloAnt. 2017, 4-11. https://doi.org/10.1145/3071178.3071239
    32. Tomas Pluhacek, Milos Petrik, Dominika Luptakova, Oldrich Benada, Andrea Palyzova, Karel Lemr, Vladimir Havlicek. Aspergillus infection monitored by multimodal imaging in a rat model. PROTEOMICS 2016, 16 (11-12) , 1785-1792. https://doi.org/10.1002/pmic.201500487
    33. Sujun Li, Haixu Tang. Computational Methods in Mass Spectrometry-Based Proteomics. 2016, 63-89. https://doi.org/10.1007/978-981-10-1503-8_4
    34. Hosein Mohimani, Pavel A. Pevzner. Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks. Natural Product Reports 2016, 33 (1) , 73-86. https://doi.org/10.1039/C5NP00050E

    Journal of The American Society for Mass Spectrometry

    Cite this: J. Am. Soc. Mass Spectrom. 2015, 26, 10, 1780–1786
    Click to copy citationCitation copied!
    https://doi.org/10.1007/s13361-015-1211-1
    Published July 21, 2015
    Copyright © 2015 © American Society for Mass Spectrometry 2015

    Article Views

    223

    Altmetric

    -

    Citations

    Learn about these metrics

    Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

    Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

    The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.