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How to group proteins within a context

Grouping is automatically saved to MSIdb. For more information on protein grouping, see here.

Load menu

Execute protein grouping

  1. Right-click one ore more context nodes of your choice in the MSIExplorer view to display context sensitive menu and select “Algorithms→Group proteins…”
  2. If needed, change settings for protein grouping (see explanations below), and Ok
  3. When grouping process is finished, the color of the context name change to red in the MSIExplorer view.


Parameters for protein grouping

Protein grouping settings:

  • Peptides having same sequence and mass are gathered together, but to avoid rejecting peptides very “close” to each other, you can specify a mass tolerance (ppm)
  • Optionnally, you can filter peptides according peptide length. For example, remove all peptides with a sequence lower than 6
  • Optionnally, you can filter proteins before grouping (this means filtering is done on protein and not protein groups !)
    • filter reverse proteins

:!: Since hEIDI 1.11.0, you can no more filter, before grouping, proteins identified with a given number of low score peptides. This filter can be applied after grouping using Peptide count protein filter.

Context where proteins are grouped have a red name

Grouping order:
If you select multiple context to group, the order of grouping will be different as the selection order. Children must be grouped before parents so the order will reflect this rule.

how_to/proteingrouping.txt · Last modified: 2012/01/23 14:29 by