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===== Analysis description ===== | ===== Analysis description ===== | ||
- | In this use case, we will work with two biological replicates (named "Replicate1" and "Replicate2").\\ | + | |
- | Each sample is aliquoted in three parts: each of them is prepared using a different separation protocol ("Ultrafiltration", "Proteominer" and "TCA Precipitation").\\ | + | In this tutorial, we will work with two biological replicates (named "Replicate1" and "Replicate2").\\ |
+ | Each replicate is aliquoted in three parts and we realize a different preparation protocol for each part ("Ultrafiltration", "Proteominer" and "TCA Precipitation").\\ | ||
Each aliquote is then deposed onto a SDS-Page gel.\\ | Each aliquote is then deposed onto a SDS-Page gel.\\ | ||
- | When separating is done, each interesting gel band is extracted and analysed using LC-MSMS. So, each band will result in one identification file ("F093496.dat"). | + | When separating is done, bands of interest are extracted from the gel and analysed using the EDyP laboratory analysis pipeline:\\ |
+ | **HPLC-MSMS -> Mascot(protein identification) -> IRMa(validation) -> MSI database(store valid identification results)**\\ | ||
+ | Each gel band will result into one identification result (named "F093496.dat" for example). Then, the analysis of a whole aliquote will generate many identification results.\\ | ||
+ | |||
+ | In the next sections, we will see how to exploit the identification results stored in the MSIdb. | ||
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===== Check the filter parameters used in identification results ===== | ===== Check the filter parameters used in identification results ===== | ||
- | FIXME verifier les paramètres de filtres des identification (how to view ident properties + .. view filter ) FIXME | + | [[how_to:idffilters|How to check filter parameters used in identification results]]\\ |
- | + | [[how_to:accessproperties|how to filter columns in a tree view]] | |
- | {{:filtersidentifications.png |}} First of all, you may want to check if your identification results have been filtered in the same way. To do this: | + | |
- | + | ||
- | * Go the the ''Identifications'' tab (you can retreive it from the main menu ''Window > Identifications''). | + | |
- | * Select multiple identifications using the ''Shift'' key (or ''Ctrl'' key for a disjoinct selection). | + | |
- | * Right-click to display the context sensitive menu and select ''properties''. | + | |
- | * A window will show up displaying all the properties for these identifications. There are different sets of properties (general properties, false pasitive, filter, etc.) and each of them can be collapsed/expanded. If ''<different values>'' appears for a given property, it means that this property is different for the group of selected identifications. If the property is the same for all the selected identifications, the property value appears.\\ | + | |
- | * Scroll down to the 'filter' category and check the filter properties you are interested in. | + | |
===== Structure your experiment as a context tree ===== | ===== Structure your experiment as a context tree ===== | ||
- | {{:usecase1_contexthierarchy.png |}} Now you need to build a context hierarchy and dispatch your identification results to map the project structure described in the first section.\\ | + | {{:usecase1_contexthierarchy.png |}} Now you need to build a context hierarchy and dispatch your identification results to map the experiment described in the first section.\\ |
See the following links to know [[userguide:contextdefinition|what is a context]] and [[how_to:createcontext|how to create a context hierarchy]]. | See the following links to know [[userguide:contextdefinition|what is a context]] and [[how_to:createcontext|how to create a context hierarchy]]. | ||
===== Execute protein grouping for every contexts ===== | ===== Execute protein grouping for every contexts ===== | ||
- | [[userguide:peptidesandproteingrouping|Protein grouping]] is the next step. [[how_to:proteingrouping|Execute the protein grouping algorithm]] for all the User contexts in a specific order.\\ | + | {{:usecase1_groupedcontexthierarchy.png |}} |
+ | A context compile a number of identifications results. A same protein may be present in several identifications. So, the first step is to suppress this redundancy by [[userguide:peptidesandproteingrouping|grouping proteins]] at the context level. [[how_to:proteingrouping|Execute the protein grouping algorithm]] for all the User contexts in this order:\\ | ||
* Start with the contexts that directly group the identification results: "Ultrafiltration", "Proteominer" and "TCA Precipitation". Do that for the two replicates. | * Start with the contexts that directly group the identification results: "Ultrafiltration", "Proteominer" and "TCA Precipitation". Do that for the two replicates. | ||
* Then continue with the contexts "Replicate1" and "Replicate2". | * Then continue with the contexts "Replicate1" and "Replicate2". | ||
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===== Browse the context tree and export it ===== | ===== Browse the context tree and export it ===== | ||
- | [[how_to:browsecontextprotgroups|How to browse a context]]. | + | [[how_to:browsecontextprotgroups|How to browse a context]].\\ |
+ | [[how_to:exportcontext|Export identified proteins from a context]]. | ||
===== Check reproducibility of results ===== | ===== Check reproducibility of results ===== | ||
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FIXME a deplacer FIXME\\ | FIXME a deplacer FIXME\\ | ||
[[how to:comparetwocontexts|How to compare contexts each other]].\\ | [[how to:comparetwocontexts|How to compare contexts each other]].\\ | ||
- | See the following link to understand [[userguide:contextcomparisons|what is context comparison]]. | + | See the following link to understand [[userguide:contextcomparisons|what is context comparison]].\\ |
+ | [[how_to:exportcomparison|Export comparison results]].\\ | ||
===== Find the optimal preparation protocol ===== | ===== Find the optimal preparation protocol ===== |