This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
how_to:proteingrouping [2009/12/17 08:29] 132.168.74.230 |
how_to:proteingrouping [2012/01/23 14:29] 132.168.72.130 |
||
---|---|---|---|
Line 1: | Line 1: | ||
- | ====== Group proteins within a context ====== | + | ====== How to group proteins within a context ====== |
- | - 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}} | + | 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'' | - 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. | - When grouping process is finished, the color of the context name change to red in the MSIExplorer view. | ||
- | {{:proteingroupingparam.png |Parameters for protein grouping}} | ||
- | | ||
+ | |||
+ | === Parameters === | ||
+ | |||
+ | {{:how_to:protgrouping.png|Parameters for protein grouping}} | ||
+ | | ||
**Protein grouping settings:** | **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) | + | * 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 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}} | {{: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. | ||