Regatta/User Guide/Reference Guide

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Contents 1 Installing 1.1 Installation manifest 1.2 Upgrading/Reinstalling 2 GUI 2.1 Menu Bar 2.1.1 File 2.1.2 Edit 2.1.3 View 2.1.4 Help 2.2 Tool Bar 2.3 Workspaces 2.3.1 Active Workspace 2.3.1.1 Mouse control on the active workspace 2.3.2 Passive Workspaces 2.3.2.1 Mouse control on the passive workspace 2.4 Display Panel 2.4.1 Stick plot 2.4.2 2D map 2.4.3 1D Gel 2.5 Methods Tabs 2.5.1 Filter Tab 2.5.2 Logic Tab 2.5.2.1 =M/=T 2.5.2.2 AND 2.5.2.3 OR 2.5.2.4 DIVIDE 2.5.2.5 XOR 2.5.2.6 UNIQUE PAIR 2.5.2.7 DYNAMIC BINNING 2.5.2.8 REFERENCE LIST 2.5.2.9 SELECT 2.5.2.10 EXCLUDE 2.5.3 Multivariate Tab 2.5.4 Reconcile Tab 2.5.5 Adducts Tab 2.5.6 Multimers Tab 2.5.7 Adjust Tab 2.5.8 Normalize Tab 2.6 Data Tables 3 Loading lists 3.1 ProTrawler .trawl files 3.2 ProTrawler .csv files 3.3 Regatta .csv files 3.4 Regatta .rgt files 3.5 Regatta. workspace files 4 Viewing Lists 5 Manipulating lists 5.1 Single lists 5.2 Pairs of lists 5.3 Multiple lists 6 Processing Wizards 6.1 Coefficients of Variation 6.2 Cluster 6.3 PCA 7 Output 7.1 Saving and Exporting 7.2 Copying to clipboard 7.3 Printing

Installing

Double click on Regatta installer. If the terms of the EULA are acceptable, then proceed with the installation. Regatta unpacks itself in c:\Program Files\BioAnalyte by default. However, it can go anywhere. Regatta requires about 20 MB of disk space, including space for documentation.

Installation manifest

• Windjammer.exe
• docs subdirectory
• icons subdirectory
• dlls
  • qt-mt332.dll
  • several Microsoft dlls what come with most operating systems, but not all

Upgrading/Reinstalling

At present, you must uninstall the existing installation of Regatta in order to make a full upgrade. This is a known issue and it is being worked on. (8/7/07)

GUI

The GUI is divided into six principal areas.

1. Menu Bar
2. Tool Bar
3. Workspaces
4. Display Panel
5. Methods Tabs
6. Data Table

Menu Bar

The menu bar functions in a familiar way.

File

Load reduced data files as either .trawl files or .csv files. Use the file browser attached to the menubar File->"Open trawl files" item or the T icon in the toolbar. One or several files may be loaded at once. Use the standard select features of the mouse and the file browser to load more than one file ProTrawler output (.trawl) files are binary and will load relatively fast.

Comma separated value (csv) files may be written and edited in Excel.

Large files (>1mb) of either type will load slowly as Regatta pre-allocates and loads all memory. After loading, all control of large data files will happen quickly.

Edit

• Copy displayed data to clipboard, (as a bitmap) to enable output to Word, PowerPoint, or other document editors.

• Copy displayed data to as ascii text clipboard, enables output to Notepad,.emacs or other ASCII editors.

View

• Workspaces, a toggle that hides/shows Workspaces
• Plots, a toggle that hides/shows Plot frame that contains x-y and 2D Map plots.
• Analytics, a toggle that hides/shows Analytics (Methods tabs)
• Data Tables, a toggle that hides/shows the tabular data.

Plot controls are self explanatory. See Tool bar documentation for more information on these.

Help

About BioAnalyte Regatta ncludes version information and company contact information.

User Guide, links to this document with a web browser.

EULA, End User License Agreement contains the legal restrictions on the use of this application.

Tool Bar

The Tool Bar reproduces much of the functionality of the Menu Bar.

Workspaces

Regatta lists are presented as Active (A) and Passive (B).

Active Workspace

Newly loaded lists are displayed in the active workspace. Each list is described by a label and a list type. Lists are assigned colors automatically; it is not possible to set colors in the current version of Regatta. List display may be turned on and off using the check box. When a list is selected, its label and type are highlighted. Selected lists are used for processing steps. N.B. List selection (highlighted labels) and display (check boxes) are unrelated.

Lists in the active workspace are available for processing by every method.

All methods require the list to be highlighted.

Mouse control on the active workspace

Right mouse options include:

• Flip Plot. This will invert the positive intensity axis for the selected plot(s) in the x-y display.
• View Audit Trail
• Save This List to RGT File, saves the list to BioAnalyte-specific RGT (binary) file.
• Save This List to CSV File, saves the list to a human/Excel readable ASCII file.
• Save Selected Lists to RGT File, saves all selected lists to the RGT format.
• Save Selected Lists to CSV File, saves all selected lists to the CSV format.
• 1D Gel View, pops-up a window containing results plotted as if they were 1D gels. This is described in greater detail in the Displays section.
• Delete Selected Lists.

Passive Workspaces

The Active Workspace is transformed into a Passive Workspace by pushing the New Workspace button. The lower frame (B) is passive. Display features are available, but no other methods.

Mouse control on the passive workspace

These are simplified versions of the Active Workspace. Selection for processing is not possible, but display checkbox=ON/OFF is enabled. Lists may be deleted, saved or copied to the Active Workspace.

• Copy highlighted items to back to Active Workspace.
• Save to file, saves select list to RGT format.
• Delete item, deletes list form workspace.
• Rename tab, renames the present workspace tab.
• Delete tab, deletes the present workspace tab.

Display Panel

There are two types of displays: stick plot and 2D map. A third type of display, the 1D pseudo gel view is available as a popup from the Workspace area.

Stick plot

• Flip plots. Select the Plot tab in the display panel. Set the display check box to ON in the Active Workspace. To flip the plot, select it in the Active Workspace and choose "flip list" from the right mouse popup menu.

2D map

Select the Map tab in the display panel. Set the display checkbox to ON in the Active Workspace. The x-axis is retention time. The y-axis is mass. The blocks are drawn to represent the rectangle given by the vertices:

• (low mass, start RT)
• (low mass, end RT)
• (high mass, end RT)
• (high mass, start RT)

1D Gel

Select list in Active Workspace. Right click and select "Display 1D pseudo- gel View.

Methods Tabs

Filter Tab

Lists my be filtered for

• mass
• retention time
• absolute intensity
• relative intensity.

Filtering is a compound process. The pop-up filter widget permits the creation of an arbitrary number of filters.

Filters on separate lines imply an logical AND relationship. The logical OR relationship may be used by selecting the OR option. Individual filters may be deleted by selecting the red X on the right. Press "Select" to engage the filter.

Filtering is accomplished by highlighting files in the active workspace.

Resulting lists are shorter than the original lists by the removal of elements that do not pass through the filter. Select one or several lists, the Filter button becomes active.

Below, you see the output from the selected files after the Retention Time filter in the above example was deleted from the filter.

Logic Tab

This series of methods implements the Transitive Property of Equality to list comparison. It represents the heart of Regatta.

These methods require the highlighting of one, two or more lists from the active workspace.

=M/=T

The equality of markers is testable in both mass and time dimensions for several logical constructs. Select one or the other or both.

AND

For two or more lists, the AND Method creates a new list consisting of markers that are in every list.

OR

For two or more lists, the OR Method creates a new list consisting of markers that occur in at least one of the selected lists.

DIVIDE

For two lists A and B, the DIVIDE Method creates two new lists consisting of A/B and B/A, where A/B is a ratio of intensities of A to B for all elements of A AND B, and visa versa.

XOR

For two lists A and B, the XOR Method creates a new list consisting of markers that exist in one list or the other, but not both (A AND NOT B OR B AND NOT A). Unlike AND and OR, XOR is not defined for more than two lists. See also UNIQUE PAIR.

UNIQUE PAIR

For two lists A and B, the UNIQUE PAIR Method creates two new lists consisting of markers that are in A AND NOT B and markers that are in B AND NOT A. See also XOR.

DYNAMIC BINNING

For N lists (N>=2), the DYNAMIC BINNING Method returns N+1 lists:

• the OR for the N lists. See OR.
• the projection of each list onto the OR list.

See dynamic binning in the Glossary.

REFERENCE LIST

For one list, this tool (not really a Method) selects the list for further comparison using the SELECT and EXCLUDE Methods.

SELECT

With one list as the REFERENCE LIST, for N (N>=1) lists, the Select Method will create N new lists consisting only of those markers present in the Reference List. This is the opposite of the EXCLUDE Method.

EXCLUDE

With one list as the REFERENCE LIST, for N (N>=1) lists, the Select Method will create N new lists consisting only of those markers NOT present in the Reference List. This is the opposite of the SELECT Method.

Multivariate Tab

Reconcile Tab

• Plot X vs. Y Deprecated and absent from the GUI as of v0.1.2.8.

• Reconcile Select 2 or more .trawl lists obtained from using different models on the same chromatogram. Then select "Reconcile". The result will be a single model that represents the collective best results from each .trawl list.

Reconcile is a Best Practice.

Multiple model reconciliation is described in Algorithms/Reconcile.

Adducts Tab

• To eliminate adduct(s) from your list(s):

1. Select/highlight the list(s) of interest.
2. Select/highlight the adduct(s) of interest.
3. Press the "Eliminate Adducts" button.

• To add new adducts to the list of available adducts:

1. Define the name.
2. Define the mass difference, e.g., '23' for sodium, but '-17' for the loss of a hydroxyl. (N.B. You may use arbitrary mass precision. These numbers are imprecise for clarity and simplicity.)
3. Press "Add to list".

• To delete one or more adducts from the list of available ones:

1. Highlight the adduct(s).
2. Press "Remove from list".

Multimers Tab

Adjust Tab

Normalize Tab

Data Tables

Loading lists

• ProTrawler CSV files. ProTrawler creates .csv and well as .trawl files. Both file types contain the same basic data. The CSV files are readable and editable by Excel. The ProTrawler CSV Format allows users to "make up their own data."

ProTrawler .trawl files

These files are created by ProTrawler.

ProTrawler .csv files

ProTrawler CSV Format files can be written by Excel or by Notepad.

Regatta .csv files

Regatta CSV Format files are nearly the same as the ProTrawler variety.

Regatta .rgt files

Regatta. workspace files

Viewing Lists

• as stick plots.
• as one-dimensional gel.
• as two-dimensional gel.

Manipulating lists

Single lists

• Normalize

There are three forms of normalization

• • Base peak. The lists are scaled so that the base peak's intensity is equal to the one given in the text box. This is useful for list-to-list display.
  • Summed intensity. The lists are scaled so that the sum of all of the intensities is equal to the one given in the text box. This is useful for multivariate analysis.
  • Unit variance. Every element in a list is rescaled independently so that the intensity uncertainty is equal to one. This is useful for signal-to-noise and significance analysis.

Multiple lists may be normalized simultaneously by selecting them in the list view area, then pressing the button associated with the type of normalization sought.

• Filter

• • Single measurable filtering
  • Multiple measurable filtering

Pairs of lists

• Reconcile
• Logic
  • XOR

Multiple lists

• Dynamically bin lists, which is a statistical alignment.

• Logical operations on lists
  • AND
  • OR

Processing Wizards

Coefficients of Variation

Cluster

PCA

Output

Saving and Exporting

Individuals lists may be saved as .rgt files or as .csv files. Files are saved from the Active Workspace using the Mouse control on the active workspace. CSV files are saved in the Regatta CSV Format .Workspaces may also be saved from the Menu Bar or the Tool Bar.

Copying to clipboard

The Tool Bar contains buttons that providing copy-to-clipboard features for exporting Regatta figures and text.

Printing

There is no direct printing mechanism in ProTrawler. To print, simply copy an image to the clipboard and paste it into another application, e.g., Word, PowerPoint or Excel.