5 XpertCalc: a Powerful Mass Calculator

The XpertCalc module is easily called by pulling down the XpertCalc menu item from the massXpert program's menu. The user is presented with a window to select the polymer chemistry definition that should be used for the calculations (Figure 5.1, “Selecting a polymer chemistry definition for use with XpertCalc”).

This figure shows that the user can either select one already registered polymer chemistry definition (listed in the drop-down widget) or browse the filesystem to select one polymer chemistry definition file. Choosing a polymer chemistry definition allows to take advantage, during the mass calculations, of all the chemical entities defined therein.

Figure 5.1: Selecting a polymer chemistry definition for use with XpertCalc #

Once the polymer chemistry definition has been correctly selected, it is parsed by the XpertCalc module and its entities are automatically made available in the calculator window, as shown in Figure 5.2, “Interface of the XpertCalc module”. The way XpertCalc is operated is very easy. This is partly due to the very self-explanatory graphical user interface of the module, which is illustrated in Figure 5.2, “Interface of the XpertCalc module”. XpertCalc can handle a number of items that are reviewed below:

It is possible to perform a set of calculations in one go, that is, the user may ask for a formula, a monomer, a modification, a sequence to be accounted in one single calculation operation. Once all the chemical entities to be taken into account have been set, the user clicks Apply: all the entities are parsed in sequence and their mass equivalent are added to the result masses. Other prominent features of XpertCalc are described in the following sections.

This figure shows that the XpertCalc polymer chemistry definition-aware module can handle atoms, formulæ, monomers, modifications and even polymer sequences for computing masses.

Figure 5.2: Interface of the XpertCalc module #

For the scientists who work on molecules that are often modified in the same usual ways, XpertCalc features a built-in mechanism by which they can easily program their calculator. This programming involves the definition of how a chemical pad (or chempad) may be arranged, exactly the same way as a desktop calculator would display its numerical keypad.

This figure shows that the chemical pad is very similar to what a numerical calculator would display. Here, the user has programmed a number of chemical reactions.

Figure 5.3: Interface of the chemical pad #

The chemical pad can be shown/hidden by using the Show Chemical Pad check box widget. An example of such a chemical pad is shown in Figure 5.3, “Interface of the chemical pad”, where a “protein-1-letter” polymer chemistry definition-associated chempad is featured. As shown, the user has programmed a number of chemical reactions that may be applied to the masses in the XpertCalc calculator window by simply clicking on their respective button (see Figure 5.3, “Interface of the chemical pad”). The configuration of the chemical pad is very easy.

Tip

It is recommended to copy one of the chemPad.conf configuration files in any of the polymer chemistry definitions distributed within massXpert and to modify it according to the instructions at the top of the file.

One example of such a configuration file is shown below along with explanations:

					color%aliceblue%240,248,255 1
					color%antiquewhite%250,235,215
					color%aqua%0,255,255

					chempad_columns%3 2

					chempadgroup%Generic 3

					chempadkey=protonate%+H1%adds a proton 4
					chempadkey=hydrate%+H2O1%adds a water molecule
					chempadkey=0H-ylate%+O1H1%adds an hydroxyl group
					chempadkey=acetylate%-H1+C2H3O1%adds an acetyl group
					chempadkey=phosphorylate%-H+H2PO3%add a phosphate group
					chempadkey=sulfide bond%-H2%oxydizes with loss of hydrogen

					chempadgroup%Hexoses & Fucose%[seagreen] 5

					chempadkey%Res-1bRE-Hexose%C6H11O6%residue Hexose (1bRE)%[lawngreen,black] 6
					chempadkey%Res-1bRE-Hexalditol%C6H12O6%residue Hexalditol (1bRE-ol)%[lawngreen,black]

These buttons might be used in two distinct ways:

Each time an action that is chemically relevant—from a molecular mass point of view—is performed, the program dumps the calculations to the XpertCalc recorder window (Figure 5.4, “The XpertCalc recorder window”). The recorder can be shown/hidden by using the Show Recorder check box widget. The text in the recorder window is editable for the user to edit the XpertCalc output, and selectable also, so that pasting to text editors or word processors is easy via the clipboard.

This figure shows that the recorder window is a simple text edit widget that records all the mass-significant operations in the XpertCalc calculator. The text in the recorder may be selected and later used in an electronic logbook or printed.

Figure 5.4: The XpertCalc recorder window #

It very often happens that the mass spectrometrist doing electrospray analyzes is faced with a challenging task: to compute by mind all the m/z ratios for a given family of charge peaks. To ease that daunting task, XpertCalc contains a m/z ratio calculator that is called by clicking onto the m/z calculation button.

The m/z ratio calculator has been described at Section 4.14, “m/z Ratio Calculations” (see Figure Figure 4.19, “Calculation of ranges of m/z ratios”.

This section is no more appropriate for version 6.0.0 and upper as it is now implemented in mineXpert2. Please refer to that software user manual.