====== How to group proteins within a context ======

Grouping is automatically saved to MSIdb.
For more information on protein grouping, see [[userguide:peptidesandproteingrouping|here]].

=== Load menu ===

{{:proteingroupingaction.png |Execute protein grouping}}
  - Right-click one ore more context nodes of your choice in the MSIExplorer view to display context sensitive menu and select "Algorithms->Group proteins..." 
  - If needed, change settings for protein grouping (see explanations below), and ''Ok''
  - When grouping process is finished, the color of the context name change to red in the MSIExplorer view.


=== Parameters ===

{{:how_to:protgrouping.png|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 [[how_to:proteinfiltering|count protein filter]]. 

{{:proteingroupingred.png|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.