peptidesandproteingrouping
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| - | ====== Protein grouping ====== | ||
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| - | ===== Algorithm ===== | ||
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| - | ==== Step 1 - Peptide grouping ==== | ||
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| - | 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 | ||
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| - | {{:GroupingStep1.png?248x148}} | ||
| - | ==== Step 2 - Protein grouping ==== | ||
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| - | 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. | ||
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| - | {{:GroupingStep2.png?271x186}} | ||
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| - | ===== 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}} | ||
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| - | **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 | ||
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| - | {{:proteingroupingred.png|Context where proteins are grouped have a red name}} | ||
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peptidesandproteingrouping.1260948777.txt.gz · Last modified: 2009/12/16 08:32 by 132.168.74.230
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