Select from Stored filters: you can create a filter in preferences and give it a name to be able to use it later for filtering. If you have any such filters, this option will list them.  Once you select the filter from the list, options below will be modified to reflect the selected filter.

 

Select Filter Category: This selection will affect the filter options listed below. GRITS currently comes with 3 filter categories (All, N-Glycan or O-Glycan filters). The user can create his/her own category in preferences to select the applicable filter options. Once a category from this drop-down is selected, only the filters listed for the selected category will be shown below.

 

AND/OR Selection: For the implications of this selection, please see examples.

 

Filter Options:

For the description of the filter, please see filter descriptions.

For each of the filters, there are 3 options: possible, yes or no.

  •       Possible – leaving a filter as "possible" means the structure may or may not have/match the corresponding filter but it will be included in the result in any case
  •       Yes – this selection means the structure must have/match the corresponding filter.
  •       No – this selection means the structure must not contain/must not match the corresponding filter
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    Range (if known):

    For some of the filters such as monosaccharide filter (Hex, GlcNAc etc.), the user can limit the number of the monosaccharide in the structure. First range option will be the minimum number required to be present in the structure (if Yes is selected, this will automatically be set to 1) and the second range is the maximum allowed. Any structure containing less than the minimum or more than the maximum will be eliminated from the result set. Leaving minimum empty (or 0) will behave as "possible" selection. Leaving maximum empty will result in any number of the selected monosaccharide (or modification etc.) being allowed in the structure.

     

    Choose how to handle "no match" cases:

    The user is given options to determine what to do in case filter causes all annotations for a certain peak (row) to be eliminated.

  •       Keep existing selections: if all annotations are filtered out, with this option, the system will keep any previous selection for that peak if any (even if that means to keep an annotation which fails to match the filter).
  •       Do not select anything: if all annotations are filtered out, this peak will be shown as an empty row (no annotations/cartoon) in the table since there are no selections.
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    Choose a criterion to use as score filter:

    In addition to above filters (or without any filter selections), the user can decide on the annotations to be selected by using a "score". Currently there are two possible scores: Intensity Score or Counting Score. 

     

    Number of Top Hits to Select:

    The user can leave it as "All" to select all possible annotations (if filter is applied then all annotations satisfying the filter) or give a number X to select the top X scoring ones (among the filtered ones if there is a filter).

     

    Override Manually Selected Annotations:

    If the user has already made selection choices in the annotation table for certain peaks then there are two options:

  •       If this checkbox is left unchecked, the filter will not make any selection changes for such peaks.
  •       If this checkbox is checked, then the filter will override the user's existing selection choices.