Results selection and settings

The page for the selection of the files can be split into for 4 parts, whereby changes in this section will just take effect in the statistics section, after the “Accept” button had been pressed.

Number 1 is for the selection of files.

- Add Files: This button allows selecting result files (Excel) for the analysis. The files appear then in the table below.
 
- Add Dir: Does the same like “Add files” but reads automatically the content of a whole directory and adds all of the Excel files in the directory to the table.
 
- Remove: Removes one ore several results from the table. The files have to be selected before in the table.
 
- Remove all: Removes all files in the table.
 
- Add to group: Is for the grouping of results. First, a set of files has to be selected in the table, and then this button has to be pressed. Then, a dialog box asks for the name of the group and the group is added to number 3, the grouping part.

Number 2 is for the sorting of the analytes. If, in the quantitation step, several analytes cannot be detected, not all of the analytes appear in the Excel results file. Then, it is hard for the algorithm to specify the correct order. At number 2, the original quantitation file can be provided. The analytes will then be displayed in the order they occur in the Excel file. The provision of the original Excel file is not mandatory, but can be helpful if several analytes were not found.

Number 3 displays the groups (they have to be selected at number 1). The grouping is not mandatory, but it can help in the interpretation of the results. Each group is displayed in a small table and the following buttons are available:

- Rename: Renames the group.
 
- Remove: Removes members of one group after they had been selected in the table where the group members are shown.
 
- Delete Group: Deletes the entire group.

Number 4 is for the selection of molecules as standard. It is assumed that the standards in the results carry a certain prefix (e.g. IS or Ex-IS). This prefix has to be entered in the two input fields. The usage of standards is not mandatory, so these fields can remain empty. If there are prefixes entered and no molecule carries these prefix, the standardization is neglected.

Number 5 is for the standardization on certain values like the protein content or the calculation of absolute values (just valid if there are standards and the ionization efficiencies of the analyte can be assumed to be similar like the one of the standards). This section is not mandatory. Before this section can be used, the results have to be selected first in number 1 and the prefixes for the standards have to be defined in number 4. Then the “Add absolute settings” button has to be pressed. The application reads now the result files and looks for standards.

The upper box of this section is for the assessment of absolute values for the standard. The box has a tab for each lipid class, so the settings can be made specifically for each class.

- use same settings for all experiments: If this checkbox is selected, it is assumed that the standards are added to each experiment at the same amounts. So a specific setting for each experiment is possible.
 
- use same settings for all standards: If this checkbox is selected, it is assumed that all of the external standards (“Ext volume” and “Ext conc.” has to be entered) and internal standards (“Int volume” and “Int conc.” has to be entered) are added at the same amounts. If not, a list of the standard appears and each standard can be entered separately.

The dilution factor corresponds to the dilution from the adding of the external standard until the internal standards are added. If the settings are entered for each experiment separately the buttons “Apply to all” and “Apply to group” appear. These buttons permit the propagation of the entered values to all experiments or to the members of a group.

The lower box is for the specification of sample specific settings like sample volume (before sample preparation) and end volume (after sample preparation). The sample volume and the end volume are mandatory, whereas the “Protein conc.” and the “Neutral lipid conc.” are not. If latter values are entered, standardization on these values is possible. The “Apply to all” and “Apply to group” buttons permit the propagation of the entered values to all experiments or to the members of a group.