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peptidesandproteingrouping [2009/12/14 16:53] 132.168.74.230 |
peptidesandproteingrouping [2009/12/16 09:16] 132.168.74.230 effacée |
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====== Protein grouping ====== | ====== Protein grouping ====== | ||
- | ===== Step 1 - Peptides grouping ===== | ||
- | Purpose:\\ | ||
- | * Group peptides from different identifications attached directly or indirectly to a context | ||
- | Critère:\\ | + | ===== Algorithm ===== |
- | * Same sequence and same experimental mass | + | |
+ | ==== 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}} | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
- | Results:\\ | ||
- | * New peptides attached to the parent context and having child peptides | ||
- | {{GroupingStep1.png}} |