====== How to export identified peptides & proteins from a context ======

===== How to access this feature =====

  * Select the context of your choice (for a User context, protein grouping should have been executed) in the MSI Explorer window 
  * Click on the menu ''MS Identification > Context > Export > Reports''
  * Select one of the five reports from the droplist (in the First Step Panel of the Assistant): 
     * **Protein groups summary**: reports the complete list of protein groups and give predefined properties for each group 
     * **Protein groups details**: reports a detailled description of all protein groups contained in the selected context 
     * **Same Subset details**: reports a detailled description of all sameset proteins and subset proteins for each protein group
     * **Peptide details**: reports a detailled description of all peptides
     * **Context customizable summary**: reports the complete list of protein groups specifying which properties to display
  * Click ''Next''
  * If you selected the "Context customizable summary" report, you have to fill in the second step panel "Customize Report" (see next section below for details). Click ''Next''.
  * In the last panel "Generate Output", select your output format (.xls, .pdf or .html) and your destination file.

{{ :how_to:exportcontext.png |}}

===== "Protein groups summary" Report =====

{{ :how_to:exportcontextsumarizeresult.png |}} 


===== "Protein groups details" Report =====

This report displays the same information as the "protein groups summary" report but also displays, for each group, the list of identified peptides.

{{ :how_to:exportcontextdetailresult.png |}}

===== "Same Subset details" Report =====

{{ :how_to:exportsamesubsetdetailsreport.png |}}

===== "Peptide details" Report =====

All PTMs are in one cell (use Tools->Text to columns and specifiy ';' as a separator to put one PTM per cell).\\
All proteins are in one cell (use Tools->Text to columns and specifiy ';' as a separator to put one protein per cell).\\
 
{{:how_to:exportpeptidedetailsreport.png|}}

===== "Context customizable summary (Protein Groups)" Report =====

For this report, a second step is necessary to select the properties to display in the final report.\\
The available property list may include user generated properties such as spectral count. \\

{{ :how_to:exportcontextcustom.png |}}