compareprotocols
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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 HPLC-MSMS+Mascot+IRMa. Each band will result in one identification file ("F093496.dat"). So, the analysis of a given replicate will generate many identification files. | + | 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 | + | A set of properties are accessible for each identification and can be [[how_to:accessproperties|displayed or used to filter the list]]. |
| + | This is specifically useful to [[how_to:idffilters|check that same filter parameters]] were used for all identification results validation.\\ | ||
| ===== 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 ===== | ||
| {{:usecase1_groupedcontexthierarchy.png |}} | {{:usecase1_groupedcontexthierarchy.png |}} | ||
| - | [[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.\\ | + | Contexts representing preparation protocol 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". | ||
| * And finally, end with the root context named "ProjectABC" | * And finally, end with the root context named "ProjectABC" | ||
| \\ | \\ | ||
| + | |||
| + | |||
| If everything has worked correctly, all the context names are now in red. | If everything has worked correctly, all the context names are now in red. | ||
| ===== 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 ===== | ||
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| ===== Compare a parent context with their child contexts and export comparison results ===== | ===== Compare a parent context with their child contexts and export comparison results ===== | ||
| FIXME a deplacer FIXME | FIXME a deplacer FIXME | ||
| - | * [[how_to:comparemultiplecontexts|How to compare a context with its children]]. | + | [[how_to:comparemultiplecontexts|How to compare a context with its children]].\\ |
| - | * Show covering diagram | + | Show covering diagram\\ |
| - | * Export results | + | [[how_to:exportcomparison|Export comparison results]].\\ |
| See the following link to understand [[userguide:contextcomparisons|what is context comparison]]. | See the following link to understand [[userguide:contextcomparisons|what is context comparison]]. | ||
| ===== Save the context hierarchy ===== | ===== Save the context hierarchy ===== | ||
| - | | + | [[how_to:savetomsidb|Save back to the MSIdb]].\\ |
compareprotocols.1262783758.txt.gz · Last modified: 2010/01/06 14:15 by 132.168.74.230
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