Any work based on CycloBranch shall cite any of the following references:


CycloBranch 1.2.495

  • Changes:
    • Image Window replaced by CrossVis tool (MALDI-MSI and DESI-MSI data can now be correlated with histology and microscopy images).
    • Waters raw data folders can now be processed (Windows only).
    • [M+Na-2H]-, [M+K-2H]-, and [M+NH4]+ ions added.
    • Single spectra can now be opened also from the Summary Table of Matched Peaks using Enter key or a row double click.
    • Filter options in Main Window, Summary Table of Matched Peaks, Building Blocks Editor, Sequence Database Editor and Modifications Editor improved.
    • Minimum Threshold of Absolute Intensity option added into the Settings Dialog.
    • Minimum Pattern Size option added into the Settings Dialog.
    • Generate Permutations of Building Blocks option removed from Settings Dialog; the feature is now always enabled.
    • Scores and FDRs of matched isotope patterns are computed for MS/MSI data.
    • Summary Table of Matched Peaks - exported statistics improved.
    • Show Isomers feature now affects Main Window, Summary Table of Matched Peaks, Spectra Details, De Novo Graph window, and HTML export.
    • Single spectrum detail window and visualization of single spectra improved.
    • Ppm error is now reported as a positive/negative number.
    • Chromatogram window added.
    • Icon sizes increased.
    • Some bugs were fixed and some other minor improvements were made.
  • Download (Windows, 64 bit - tested on Windows 7/10)
  • Download (Linux, 64 bit - tested on Ubuntu 16.04)
  • Download (macOS, 64 bit - tested on macOS 10.12 Sierra)
  • PDF manual
  • Download Sources (Windows)
  • Download Sources (Linux)
  • Download Sources (OS X)
  • Additional databases: Lipids


CycloBranch 1.2.192


CycloBranch 1.1.570


CycloBranch 1.1.170


CycloBranch 1.0.1512


CycloBranch 1.0.1216

  • Changes:
    • Export of graphical visualization of spectra and peptides into SVG fixed for Windows.
    • Feature added: show/hide isomers of building blocks in the output report.
    • Bug fixed: HTML report was exported incorrectly when the order of rows was changed.
    • Quit confirmation dialog added.
    • Names of precursor ions of multiply charged ions and precursor ions with adducts fixed for MS/MS spectra.
    • Peptide identification details in the main window can be also opened using Return/Enter key.
    • Image export dialog improved in the spectrum detail window.
    • Find text option added into the spectrum detail window.
    • Similarity search can be performed when a peklist is searched against a database of MS/MS spectra.
    • Monoisotopic masses of sequence candidates are now reported in the main window.
    • Settings dialog was improved for monitors with small resolutions (scrollbars added).
    • Export of PS images dropped in Linux (PDF files were generated instead of PS files; pdf2ps tool is now recommended to generate PS files).
    • OS X is now supported.
    • A text filter of rows was added into the main window, building blocks editor, sequence database editor and modifications editor.
    • Save confirmation dialogs added into editors when closing editors.
    • The internal periodic table has been extended.
    • Some bugs and performance issues fixed.
  • Download (Windows, 64 bit - tested on Windows 7/8)
  • Download (Linux, 64 bit - tested on Ubuntu 14.04)
  • Download (OS X, 64 bit - tested on OS X 10.8 (Mountain Lion))
  • Download Sources (Windows)
  • Download Sources (Linux)
  • Download Sources (OS X)


CycloBranch 1.0.1106


CycloBranch 1.0.850

  • Changes:
    • Database search added (for MS and MS/MS spectra).
    • Databases of building blocks updated.
    • Building blocks editor added.
    • Sequence database editor added.
    • A number of paths in a de novo graph forming sequence candidates is calculated before the search.
    • The version of the application is checked when a results file (*.res) is opened.
    • Number of matched scrambled fragment ions is reported when a cyclic peptide is searched.
    • Small bugs fixed.
  • Download (Windows, 64 bit)
  • Download Sources (Windows)


CycloBranch 1.0.739


CycloBranch 1.0.696