CycloBranch
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21.8.2023

CycloBranch 2.1.35

10.8.2022

CycloBranch 2.1.21

  • Changes:
    • Quantification of compounds in LC-MS datasets is now possible.
    • "Annotated Features Overview" added (a table of all features matched in all LC-MS files).
    • "Simulate Isotopic Pattern" feature added.
    • "Calculate Molecular Formula" feature added.
    • The names corresponding to molecular formulas of compounds identified in "Compound Search - MS, LC-MS, MSI" mode can now be searched in PubChem.
    • The range of retention time can now be limited in the settings dialog if LC-MS data is processed.
    • Retention time of individual database compounds can also be limited if LC-MS data is processed.
    • "Minimum Intensity of Highest Peak in Isotopic Pattern" parameter was added into the Settings dialog.
    • "54Fe/56Fe Ratio" parameter was added into the Settings dialog.
    • Line/Profile mass spectra can now optionally be converted by CompassXtract from baf files.
    • Waters data support improved.
    • EIC chromatogram is now visible by default.
    • Calculation of FDRs (LC-MS and MSI data) can optionally be disabled.
    • Copy to clipboard function (CTRL+C) improved in Building Block, Sequence/Compound, and Modification editors.
    • Remove duplicate rows feature added in Sequences/Compounds Editor.
    • Export matched formulas to a compound database - feature available in "Summary Table of Matched Peaks" and "Annotated Features Overview" if "Compound Search - MS, LC-MS, MSI" mode was used.
    • Results files (*.res) are now backwards compatible (starting from version 2.0.8).
    • Data processing tab added in Preferences dialog.
    • Compounds in NP Atlas and COCONUT can now be referenced from Sequence/Compound Editor.
    • Bookmarks toolbar was added and corresponding tab was fixed in Preferences dialog.
    • Unused parameters are now automatically hidden in the Settings dialog.
    • Multiple LC-MS files can now be processed in a batch.
    • Multiple threads can now be used if LC-MS or MSI data are processed.
    • Image fusion improved:
      • Current configuration of layers can now be loaded/saved.
      • Open image function was improved.
      • Import dialog was added to open a batch of microscopy images FEI (SEM) / Leica (optical and fluorescence).
      • Optical and fluorescence microscopy images can now be opened directly from *.lif files (Leica).
      • Horizontal and vertical flip feature added for microscopy images.
      • Name and magnification is now visible for every microscopy layer.
      • Navigation buttons were added to browse microscopy layers (Previous, Next).
      • Maximum number of microscopy layers was increased to 200.
      • A dropdown menu was added to change the navigation layer of any microscopy layer.
      • Keep aspect ratio feature added when resizing a region (CTRL + resize by mouse).
      • Clear all/individual layers features added.
    • Some other minor bugs and performance issues were fixed and minor improvements were made.
  • Download (Windows, 64 bit - tested on Windows 10)
  • Download (Linux, 64 bit - tested on Ubuntu 20.04)
  • Download (macOS, 64 bit - tested on macOS 10.12 Sierra)
  • Download Sources (Windows)
  • Download Sources (Linux)
  • Download Sources (OS X)
  • Additional databases: Lipids

11.3.2020

CycloBranch 2.0.8

20.11.2019

CycloBranch 2.0.0

  • Changes:
    • Compound search mode added (a database-free search mode for MS1, LC-MS, and MSI data).
    • Fragmentation of metabolites is now supported (peptide type "Other" in MS/MS mode).
    • A list od neutral losses can now be defined for individual building blocks.
    • The databases of blocks were updated to a new file format (the column neutral losses was added).
    • Spectrum detail window can now be opened direcly from chromatogram or image fusion window by a double-click.
    • Filter options improved - main window, summary table of matched peaks, and editors (building blocks, sequences/compounds, and modifications).
    • Processing of Waters data improved and visualization of profile data added.
    • Visualization of profile mzML/Thermo raw files added and a bug fixed during profile data processing.
    • Retention time is now reported for LC-MS data.
    • Minimum number of spectra can now be defined for LC-MS and MSI data.
    • Minimum number of matched ions can now be defined for MS, LC-MS, and MSI data.
    • New parameters added: Basic Formula Check, Advanced Formula Check, N/O Ratio Check, Isotope m/z Tolerance, and Isotope Intensity Tolerance.
    • Percentage contributions of peak components (e.g. 13C, 17O) are now reported if theoretical isotopic patterns are calculated.
    • Copy to clipboard function (CTRL+C) improved in spectrum detail window, main window, and summary table of matched peaks (multiple rows and columns can be selected in the table).
    • Visualization of mass spectra fixed (occasional flashing).
    • A bug fixed - existing items in the list of neutral losses were not editable if the settings dialog was re-opened.
    • A bug was fixed when too many combinations of neutral losses were generated.
    • Internal ions can now be generated for branch-cyclic peptides.
    • DOI can now be used as a reference in a compound/sequence database.
    • [M+Cl]- ion added in MS mode.
    • Link to BBDGNC added.
    • zlib compression is now supported in mzML files.
    • Some other bugs were fixed and minor improvements were made.
  • Download (Windows, 64 bit - tested on Windows 7/10) (updated 29.4.2020)
  • Download (Linux, 64 bit - tested on Ubuntu 16.04)
  • Download (macOS, 64 bit - tested on macOS 10.12 Sierra)
  • Download Sources (Windows)
  • Download Sources (Linux)
  • Download Sources (OS X)
  • Additional databases: Lipids

22.5.2018

CycloBranch 1.3.1

  • Changes:
    • Spectrum detail window improved:
      • Profile spectra can now be visualized.
        • Bruker's baf files on (Windows only)
        • imzML
      • Visualization of mass spectra improved.
      • Hide labels of peaks feature added.
      • Mouse wheel function improved.
      • Summary formulas of experimental peaks are now reported also in MS/MS mode.
      • An experimental peak can now be focused in using a double-click.
    • Chromatogram - visualization and mouse wheel function improved.
    • Summary Table of Matched Peaks - an experimental peak can now be focused using a double-click.
    • "Compare Peaklist with Database - MS/MS data" mode - a bug fixed; different theoretical spectra with the same score were reported only once.
    • LC-MS/MS data - all spectra in a dataset are now compared with a theoretical spectrum of a searched sequence if "Compare Peaklist(s) with Spectrum of Searched Sequence" mode is used (the parameter "Scan no." is not used in this mode).
    • Settings dialog - layout fixed for macOS.
    • FileConverter - collision of filenames between OpenMS and Xcalibur fixed.
  • 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)
  • Download Sources (Windows)
  • Download Sources (Linux)
  • Download Sources (OS X)
  • Additional databases: Lipids

26.2.2018

CycloBranch 1.2.748

  • Changes:
    • A custom list of neutral losses can now be defined for MS, MSI and MS/MS data.
    • Details of MS/MS spectra improved - matched peaks can now be filtered using a name of a ion series or using name of a neutral loss.
    • Settings dialog improved:
      • "Neutral Losses" - a modifiable list added.
      • "Maximum Number of Combined Losses" - settings added.
      • "Report Unmatched Theoretical Peaks" - checkbox added; performance improved if unchecked.
      • "m/z Error Tolerance for Deisotoping" - obsolete feature removed.
      • "Remove Hits of Fragments without Hits of Parent Fragments" - obsolete feature removed.
      • Obsolete scoring functions removed.
    • Unmatched theoretical isotope patterns can now be reported in MS, MSI and MS/MS mode.
    • Memory performance was improved.
    • OpenMS 2.3 is now supported.
    • Thermo raw files are now supported.
    • mzML support improved.
    • [M]+, [M]- ions added.
    • Bug fixed: the number of electrons was wrong if the m/z ratio of negative ions was calculated in "Generate Full Isotope Patterns" mode.
  • 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)
  • Download Sources (Windows)
  • Download Sources (Linux)
  • Download Sources (OS X)
  • Additional databases: Lipids

15.12.2017

CycloBranch 1.2.660

  • Changes:
    • De novo sequencing improved - sequence candidates with the same score and identical path in the de novo graph are now reported only once.
    • Summary formulas of fragment ions are now reported.
    • Fine isotope patterns of fragment ions are now generated.
    • Visualization of mass spectra and chromatogram improved - they can be shifted left/right by mouse now.
    • The list of peaks in a spectrum detail window can now be filtered using a ring break-up point (cyclic peptides) or linearized sequence type (branched peptides).
    • Image Fusion - support of microscopy images fixed; image export fixed; pixel width and height fields added.
    • Summary Table of Matched Peaks - calculation of statistics fixed.
    • Multiply dehydrated and deamidated fragment/precursor ions are now reported.
    • imzML support improved.
    • CompassXPort support improved.
    • [M+Si-3H]+, [M+Si-4H+Na]+, [M+Si-4H+K]+, and [M+Si-5H]- ions added.
    • Some minor bugs were fixed and performance was improved.
  • 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)
  • Download Sources (Windows)
  • Download Sources (Linux)
  • Download Sources (OS X)
  • Additional databases: Lipids

22.6.2017

CycloBranch 1.2.495

  • Changes:
    • MALDI-MSI and DESI-MSI data can now be correlated with histology and SEM 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)
  • Download Sources (Windows)
  • Download Sources (Linux)
  • Download Sources (OS X)
  • Additional databases: Lipids

3.10.2016

CycloBranch 1.2.192

19.5.2016

CycloBranch 1.1.570

15.12.2015

CycloBranch 1.1.170

21.9.2015

CycloBranch 1.0.1512

15.5.2015

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)

3.3.2015

CycloBranch 1.0.1106

19.11.2014

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)

3.10.2014

CycloBranch 1.0.739

3.9.2014

CycloBranch 1.0.696