how_to:proteingrouping
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how_to:proteingrouping [2010/01/04 17:04] 132.168.74.230 |
how_to:proteingrouping [2012/01/23 14:29] (current) 132.168.72.130 |
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| ====== How to 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. | ||
how_to/proteingrouping.1262621055.txt.gz · Last modified: 2010/01/04 17:04 by 132.168.74.230
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