In Byos, there are several ways to filter Peptides, Modifications, or others attributes.
In the Peptides Table you can see 3 different locations where you can filters:
- magnifier icon
- Column Filter; BottleNeck icon
- Text filter search box
- Right-Click Context menu
The Peptide type filter tab allows the inclusion or exclusion of peptide modification types. Check modifications to include and uncheck modifications to exclude. Byologic defaults to all peptide types:
Figure : Filtering by peptide type
The Search filter options are considered to be hard filters. The filtered out rows are not shows in the protein coverage view, are excluded from "add missing via existing" function, and do not appear in the reports.
To save the edited settings from the two tabs to a configuration file, click the Save Preset button, enter a file name, navigate to a directory, and click Save. To load settings from a previously-saved configuration file, click the Load Preset button, navigate to the desired directory, select a *.blgcsfson or *.blgcsf file, and click Open
The Text filter search box can be used to search for specific values or variables in the entire Peptides table, with options to filter for only whole values, with case-sensitivity, and to only search in vertical header columns.
Filtering example: DTLIMISR search box
The filter icon opens the Column Filters Editor dialog. The dialog enables filtering based on combinations of column values:
Figure : Column Filters Editor for filtering data to plot
Column filters are soft filters that do not automatically update protein coverage view or the reports, although both can be configured to take into account column filters (protein coverage view via its cogwheel settings button, reports via Tabs menu->Update tab content.) Similarly, any peptides filtered out via column filters would be considered for the "add missing via existing" action.
Eg. Filtering “Var. Pos. Protein” and “Var. Pos. Peptide”
The values in "Var. Pos. Protein" and "Var. Pos. Peptide" columns during filtering are treated as a list of integers. For these columns only the list of integers (integers separated by a comma) is acceptable when entering filter conditions in the dialog
Figure : Filter by Var. Pos. Protein and Peptide
If a non-integer value is entered, the user will receive an error message to correct the value entered, as shown below.
Figure : Var. Pos filtering requires integers
On the bottom left corner, there is a Presets button which shows multiple options for saving and loading filter sets as presets. Below is an example of a column filter which remove peptide sequences which contains "UNK" (for unknows) and save within the project.
Table Right-Click Menus
The Project, Protein Coverage, Peptides, and Wildtype peptides tables have context menu items revealed by a right-click on the rows within the tables.
Table context menus contain a set of query options for searching the clicked text value using any of the available search operators. This is an easy way to filter a table based on a specific field value
Figure : Search table values through a right-click menu
Effectively, the right-click menu applies a column filter. The selected values and filters can be edited using the column filters option as above.