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We will analyse two biological replicates (named “Replicate1” and “Replicate2”).
Each sample is aliquoted in three. The three aliquotes are prepared using different separation techniques (“Ultrafiltration”, “Proteominer” and “TCA Precipitation”).
Each “prepared” aliquote is deposed onto a 1D 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”).
...Project ABC ...Replicate1 .Ultrafiltration .F093496.dat .F093497.dat ... .Proteominer ... .TCA Precipitation ... ...Replicate2 .Ultrafiltration ... .Proteominer ... .TCA Precipitation ...
Please follow the steps in the getting start to setup the MSI db connection (Mass Spectrometer Identification database), create an hEIDI project and open a working session on the MSI db.
verifier les paramètres de filtres des identification (how to view ident properties + .. view filter )
First of all, you may want to check if your identification results have been filtered in the same way. To do this:
Identifications
tab (you can retreive it from the main menu Window > Identifications
).Shift
key (or Ctrl
key for a disjoinct selection).properties
. <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.
Now you need to build a context hierarchy and dispatch your identification results to map the project structure described in the first section.
See the following links to know what is a context and how to create a context hierarchy.
Protein grouping is the next step. Execute the protein grouping algorithm for all the User contexts in a specific order.
If everything has worked correctly, all the context names are now in red.
You may want to compare results from the same preparation protocol in the two replicates.
How to compare contexts each other.
See the following link to understand what is context comparison.
You may want to compare protocols each other for a given replicate to find the “best” one.
See the following link to understand what is context comparison.