Biograph’s components can be grouped into three major components: the Title Panel, the Tool Results Panel and the Spectrum Manipulation Panel (see Fig. 2).

Fig. 2 Shows Biograph Applet for PeptIdent tool

The title panel of Biograph shows information such as the name of the user entered protein, among others; the Tool Results Panel shows the results specific to Peptident, FindPept or FindMod and an option for saving matching mass lists. On the right side, the spectrum manipulation panel shows the user entered spectrum in a graphical way with various tools for analysis. Each of these regions and their corresponding subcomponents are described below.

C.1. Title panel

As shown in Fig. 3, Biograph Applet v2.0 presents the following information to the user:

- Source tool name: the tool from which the call to Biograph v2.0 applet was generated, i.e. PeptIdent, FindPept or FindMod

- User entered protein name: the name given to the user entered protein.

- Date&Time: the date and time PeptIdent or SmartIdent result was generated.

In Fig. 3 we can see that Biograph Applet v2.0 was called from PeptIdent tool, given the user protein sequence Human Protein in 1/22/02 at 4:50 PM.

Fig. 3 The Title Panel with some information on a query to ExPASy software.

C.2. Tool Results Panel

This panel shows information found by an Expasy tool. The information showed depends on the tool from which Biograph was invoked. The following figures shows this panel for different tools.

Fig. 4 Tool Results Panel for PeptIdent

Fig. 5 Biograph Applet for FindPept

Fig. 6 Biograph Applet for FindMod

The Tool Results Panel contains results from PeptIdent, FindPept or FindMod.

• For PeptIdent as shown in Fig. 4, it shows a table of matched proteins, which can be selected or unselected by clicking on any row of the table. Last selected matched protein are in red and all other selected proteins are in blue. When selecting a protein, its corresponding peaks are painted with the same color in the spectrum manipulation panel.
• For FindPept tool (Fig. 5), the Tool Results Panel shows four options that can be selected/unselected by clicking on the checkbox. When selecting an item, the peaks that belong to the item are painted with the same color as the item selected.
• For FindMod tool (Fig. 6), four options are shown and the user can select or unselect any of them. The same action of painting the peaks is done as for FindPept.

C.3. Spectrum manipulation panel

It’s important to graphically see the user entered spectrum, manipulate it and see information on each and every one of its peaks. The spectrum manipulation panel contains three basic components for these purposes, in Fig. 7: the toolbar, the spectrum panel and the information panel.

Fig. 7 Three general components for the spectrum visualization panel.

The information panel shows information on any particular peak. The toolbar allows the user perform some operations over the spectrum that is being displayed in the spectrum panel. All these elements are described below.

C.3.1.The toolbar

The toolbar contains eight (8) buttons (see Fig. 8) which are used to perform certain tasks with the spectrum that is being shown in the Spectrum Panel component.

Fig. 8 Biograph Applet v2.0 ToolBar.

Two (2) buttons are used for printing the user entered spectrum:
- Print Button: prints the content of the spectrum area.
- Print Preview Button: displays a preview of what will be printed.

Five (5) buttons are related to the manipulation of the user entered spectrum:
- Hand Tool Button: allows the user to move the user entered spectrum in the horizontal-axis (the m/z axis).
- Zoom-in Tool Button: zooms in the spectrum in the horizontal-axis.
- Zoom-out Tool Button: zooms out the spectrum in the horizontal-axis.
- Zoom Window Tool Button: allows to choose an arbitrary regin and zoom that region in the x-axis.
- Peak Distance Tool Button: provides the mechanism to compare any of two given peaks in the spectrum.

By clicking one of these buttons makes it remain selected until the mouse button is pressed again over it or other of the five buttons is clicked. The clicked state means that the user can apply the operation the button indicates multiple and consecutive times. That’s why these options are usually referred by the name “tools”, and when one button is in a clicked state it’s said that “the tool is selected”. For example, if the user clicks over the Hand Tool Button the user can move the spectrum along the horizontal-axis (the m/z axis) as many as he/she desires using the mouse buttons. In a two or three button mouse, the user can use the left and right buttons, for one button mice there is no other option but to use the only button available. This is the way the other tools operate too. Although, one tool, the Zoom Window Tool doesn’t follow the former rule, a click with the right button undoes the operation while pressing the left button performs the operation pointed out by the button.
Finally, one button, the Help Button provides a link to Biograph Applet v2.0 online help.

C.3.2. The spectrum panel

This panel is used for displaying the user entered spectrum. The operations performed by means of one selected tool (one of the five tool buttons) modify the appearance of this panel. For instance, if the user chooses the zoom-in tool, then one click over the panel makes the spectrum zoom a certain factor in the horizontal axis. In Fig. 9 we can see that the spectrum has been zoomed-in certain times, so that the m/z values are in the hundreds now, being in the thousands before.

Fig. 9 The Axes and the spectrum drawing.

Besides displaying the user entered spectrum, this panel contains two rules for an easy estimation of m/z and intensity values for peaks.

C.3.3. The peak information panel

This panel shows information on every peak the mouse pointer passes over the peak’s selection area (the red box on top of it).

Fig. 10 Peak Information Panel for PeptIdent

In Fig. 10 we can see that the mouse pointer entered the selection box of a peak with m/z equal to 545.322 and Intensity of 43. This peak is selected, thus, information on the matching peptides in the theoretical proteins are displayed. The information shown depends on the tool. For example, Figure 10 shows protein AC, protein ID, peptide mass, delta mass, missing cleavages, modifications, position in the protein and the peptide sequence. For FindPept and FindMod, the information shown is extracted from the results page of each tool.

From Fig. 10, the first row shows information of one of the matching peptides: it belongs to protein Q15149 (PLE1_HUMAN), its mass is 545.304 (a delta mass of –0.0180 comparing to the user entered peak mass), it has 0 missing cleavages, no modifications (the symbol ? indicates that), its starting position in the protein sequence is at 1383 and its ending position is at 1386 (its length is 4),finally, its sequence is EQLR.