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peptidesandproteingrouping [2009/12/15 11:13] 132.168.74.230 |
peptidesandproteingrouping [2009/12/16 09:16] 132.168.74.230 effacée |
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Peptide grouping results in **new** peptides attached to the parent context and having child peptides | Peptide grouping results in **new** peptides attached to the parent context and having child peptides | ||
- | {{proteinGrouping:GroupingStep1.png?248x148}} | + | {{:GroupingStep1.png?248x148}} |
==== Step 2 - Protein grouping ==== | ==== Step 2 - Protein grouping ==== | ||
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Protein grouping results in **new** groups of proteins and peptides, attached to the parent context. | Protein grouping results in **new** groups of proteins and peptides, attached to the parent context. | ||
- | {{proteinGrouping:GroupingStep2.png?271x186}} | + | {{:GroupingStep2.png?271x186}} |
===== GUI - Execute protein grouping algorithm ===== | ===== 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}} | ||
+ | | ||
- | - Right-click on the context node of your choice in the MSIExplorer view to display context sensitive menu and select "Algorithms->Group proteins..." {{ :proteingrouping:proteingroupingaction.png|Execute protein grouping}} | + | **Protein grouping settings:** |
- | - Change parameters for protein grouping if needed. Validate. | + | |
- | - When grouping is finished, the color of the context name change to red in the MSIExplorer view. | + | |
- | + | ||
- | + | ||
- | {{:proteingrouping:proteingroupingparam.png?350 |Parameters for protein grouping}} | + | |
* 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) | * 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 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 | * 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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