CycloBranch
Main Window and Toolbar

Main Window

Main window of the application.

File

Open Results... (CTRL + O)

Open an output report (a file *.res).

Save Results... (CTRL + S)

Save an output report (a file *.res). Files created using an older version of the software cannot be opened in a newer version.

Export to CSV (CTRL + Shift + C)

An output report is exported into a csv (comma separated values) file and it can be imported, e.g., to MS Excel.

Export to HTML (CTRL + Shift + H)

An output report is exported into a HTML page.

HTML Export Dialog.

Summary:

  • Parameters - export the search parameters
  • De Novo Graph - export the de novo graph (if "De Novo Search Engine" Mode was used)
  • Log Window - export the content of Log Window
  • Output Report Table - export the Output Report in the main window
  • Summary Table of Matched Peaks - export the summary table of matched peaks; see Summary Table of Matched Peaks

Individual Rows in Output Report (the following data are exported for each row in the table):

  • Peaks Table - export a table of peaks
  • Unmatched Experimental Peaks - export unmatched experimental peaks
  • Unmatched Theoretical Peaks - export unmatched theoretical peaks (MS/MS data only)
  • Details of Identification - export identification details (MS/MS data only)

The tables in the output report can be sorted using any column. This feature uses jQuery and requires an on-line connection. If the feature does not work, the following paths in a source code of the generated HTML report must be fixed: 

https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.4/jquery.min.js
https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.23.3/js/jquery.tablesorter.min.js
https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.23.3/css/theme.green.min.css

Preferences (CTRL + Shift + P)

Global preferences of the application. See details here.

Quit (CTRL + Q)

Quit the application.

Search

Run (F5)

Run the application using predefined settings.

Stop (F6)

Stop the computation if running.

Settings... (F7)

Settings of the application. See details here.

Tools

Building Blocks Editor (CTRL + B)

An editor of a database of building blocks is opened. See details here.

Sequence/Compound Database Editor (CTRL + D)

An editor of a database of sequences is opened. See details here.

Modifications Editor (CTRL + M)

An editor of a list of modifications is opened. See details here.

Draw Peptide (CTRL + P)

The "Draw Peptide Tool" is opened. See details here.

Summary Table of Matched Peaks (F8)

Show a summary table of matched peaks reported in all rows which are currently listed in the main window. See details here.

Chromatogram (F9)

Show a chromatogram for LC-MS data. See details here.

Image Fusion (F10)

Open the image fusion tool. See details here.

Simulate Isotopic Pattern (F11)

Open the simulate isotopic pattern tool. See details here.

Calculate Molecular Formula (F12)

Open the calculate isotopic formula tool. See details here.

Bookmarks

A custom list of up to 10 bookmarks can be created in global Preferences dialog. The bookmarks can then be opened in an external web browser using CTRL + 1, CTRL + 2, ..., CTRL + 9, and CTRL + 0. See details here.

View

Show Isomers (CTRL + I)

Show/hide isomers of building blocks.

De Novo Graph (CTRL + G)

Open a window with the de novo graph. The graph is updated dynamically when the engine is running in "De Novo Search Engine" mode.

A de novo graph.

Log Window (CTRL + L)

Enable/disable the log window with the current status of the application.

Log window.

Help

HTML Documentation (F1)

This documentation is opened from the local file 'docs/html/index.html'.

PDF Manual (F2)

The PDF manual is opened from the local file 'docs/refman.pdf'.

About (F3)

An about dialog of the application is shown (a version number, licence information, etc.).

Text Filter

See details here.