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--- peptidesandproteingrouping [2009/12/16 09:16]
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-====== Protein grouping ======
-===== Algorithm =====
-==== Step 1 - Peptide grouping ====
-Peptides from different identifications - attached directly or indirectly to a context - are grouped.\\
-Peptides must have same sequence and same experimental mass to be grouped.\\
-Peptide grouping results in **new** peptides attached to the parent context and having child peptides
-{{:GroupingStep1.png?248x148}}
-==== Step 2 - Protein grouping ====
-Peptides from a same protein or a same protein set are grouped.\\
-Protein grouping results in **new** groups of proteins and peptides, attached to the parent context.
-{{:GroupingStep2.png?271x186}}
-===== GUI - Execute protein grouping algorithm =====
-  - Right-click on the context node of your choice in the MSIExplorer view to display context sensitive menu and select "Algorithms->Group proteins..." {{ :proteingroupingaction.png|Execute protein grouping}}
-  - If needed, change settings for protein grouping. Validate.
-  - When grouping process is finished, the color of the context name change to red in the MSIExplorer view.
-  {{:proteingroupingparam.png?350 |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 reverse proteins and/or proteins identified with a given number of low score peptides
-{{:proteingroupingred.png|Context where proteins are grouped have a red name}}

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