You may have already seen that many operations can be performed while working with Biograph Applet v2.0. In this section those operations are explained in detail showing how the various parts of Biograph Applet v2.0 connect.

D.1. Selecting/unselecting Matched Proteins for PepIdent Tool

As mentioned earlier, the user can select/unselect matched proteins by clicking anywhere on any the rows of the the Matched Proteins Table (see Fig. 4). The just selected protein becomes red (the corresponding row background is painted in red) and the former last protein which was blue, if any, becomes blue. Two labels under the table indicates the user which colour correspond to the selected proteins and which one to the last selected protein. Non-selected proteins have their corresponding rows backgrounds set to white.

For PeptIdent, user entered spectrum peaks that are displayed in the Spectrum Manipulation Area and that match any of the selected proteins, are painted with the colour of the protein (blue or red), and are said to be selected as well. So the user can identify which of his/her entered peaks match peptides in one or more theoretical proteins. Moreover, by placing the mouse pointer over a selected peak’s selection box, information on the matching peptides is displayed in the Peak Information Panel.
In Fig. 11 you can see that there are two selected theoretical proteins, one in blue and the other in red (the last selected).

Fig. 11 Proteins Q99996(Isoform) and Q15149 are selected. (PeptIdent tool)

D.2. Visualizing Information on peaks

The user can have information available for each peak displayed in the Peak Information Panel by simply placing the mouse cursor over the peak’s selection area (the red box on top of each peak) in the Spectrum Manipulation Panel. If the peak matches any peptide in the Tool Results Panel, all the matching peptides information is displayed, as you can see in Fig. 12 and Fig. 13. On the other hand, if the mouse cursor is over a peak that doesn’t match any peptide (i.e. if peak is black), only do the m/z and intensity values are displayed for it.

Fig. 12 Peak P1 matches a peptide in protein P12111, the latter being the last selected protein.

Fig. 13 Peak P2 matches a peptide in protein P51587.

D.3. Creating mass lists

When the user wants to export the peaks that match some of the theoretical proteins, he/she can perform that using this option, by simply pressing the “Create mass list for” button, see Fig. 14. Two matching peaks subsets can be saved, selected matching peaks (choose “Selected” radio button) and unselected matching peaks (choose “Unselected” radio button). When button is clicked, a new window will prompt the user for a location and file name to save file. The file is in DTA format.

Fig. 14 Create mass list option.

D.4. Print and Print Preview

What can be printed is the user spectrum that is being displayed in the Spectrum Panel. The options for having a print-preview and print the document are available in the toolbar, as it was earlier stated (Fig. 8).
When the user chooses to have a print preview of the Spectrum Panel, the user is prompted a dialog and he/she can choose to cancel or print what is being displayed (see Fig. 15).

Fig. 15 Print Preview Dialog in Biograph.

When the user chooses the Print option, then a print dialog is displayed (by means of the Print button in the Print Preview dialog or the Print Button in the Toolbar). This dialog depends on the platform, for example in Fig. 16, the dialog displayed is under Windows XP.

Fig. 16 The print dialog.

D.5. Moving the user spectrum in the pane

When the spectrum is zoomed, the user can choose the Hand Tool ( Fig. 8) for moving it across the panel. Once the tool is selected, the user moves the spectrum by pressing the mouse button (left or right, or the only button available) without releasing it and moving the mouse from left to right and vice versa. To stop moving the spectrum, the user only needs to release the mouse button. The following sequence shows this process (Fig. 17, Fig. 18, Fig. 19 and Fig. 20).

Fig. 17 The user clicks over the Hand Tool Button.	Fig. 18 The Hand Tool Button remains pushed.
Fig. 19 The spectrum is moved to the right.	Fig. 20 The spectrum is moved to the left.

D.6. Zoom-in and Zoom-out

In Biograph, the user can zoom-in and zoom-out the spectrum only in the m/z axis (the horizontal axis) by choosing the zoom-in or zoom-out tool Buttons available in the toolbar (Fig. 8).
The zoom process is centered around the mouse position, this means that the point where the user clicks remains static and the other points to the left and to the right are adjusted accordingly. The only exception to this, is when the user is performing a zoom-out process, and the spectrum is approaching its original size (all peaks are visible). A sequence for a zoom-in process is shown in Fig. 21, Fig. 22 and Fig. 23.

Fig. 21 The user selects the zoom-in option.

Fig. 22 The mouse is positioned to the left part of the spectrum.

Fig. 23 A click is performed and the zoom takes place.

Something similar occurs if the user selects the zoom-out tool.

D.7. Visualizing a specific region

Zooming the spectrum a fixed factor is something desired, but many times the user wants to see an specific region in the spectrum, an m/z interval within the current visible m/z interval. A tool is available for this task, the so-called “Zoom Window Tool”. By choosing this tool, the user can select a region by pressing the left mouse button (or the only available mouse button) and moving the mouse to select the desire area to visualize, a red square will guide the user to this end. An example of this process is shown in Fig. 24, Fig. 25, Fig. 26 and Fig. 27.

Fig. 24 The Zoom Window Tool is chosen.	Fig. 25 A click on the spectrum panel displays the starting red line.
Fig. 26 Moving the mouse without releasing its button defines an area	Fig. 27 Releasing the mouse button makes the defined area to be entirely visible in the panel.

D.8. Comparing any of two peaks

To know the differences between any of two peaks, the user can choose the “Peak Distance Tool”. The user clicks over one peak (over its selection box), making it the reference peak and later can position the mouse over other peaks and see their differences one by one with the reference peak. A sequence for this process is shown in Fig. 28, Fig. 29 and Fig. 30.

Fig. 28 The peak distance tool is chosen.

Fig. 29 A click over a peak’s selection box makes it the reference peak and displays a panel showing its basic information

Fig. 30 The mouse pointer is moved to the selection box in other peak, the differences in m/z and intensity values are displayed in the panel at the top.

D.9. Getting some help

By clicking over the help button in the toolbar (Fig. 8) launches a new browser window where help on Biograph Applet v2.0 is available. See Fig. 31 for a sample on this.

Fig. 31 Biograph online help is launched.