====== Generate a new AMT database from a context ======

:!: **Requirements** \\
  * Context have to be **[[how_to:proteingrouping|grouped]]** previously. You generally apply some filtering during and/or after the protein grouping step to suppress:         
    * Reverse proteins
    * Species with a sequence < 7
    * Proteins identified by only 1 species with a score < 60
  * **[[how_to:alignretentiontime|Retention time alignment]]** & **[[how_to:recomputeretentiontime|retention time recomputing]]** algorithms may have to be run before creating
  * Save your MSIdb
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To generate a new AMT database in the MS Access format (.mdb file) from a given User context, follow these steps:

{{ :amtexport_menu.png|Export a context to a new AMT database}}

  * Select the User context you want to export
  * Select ''MS Identifications > Context > Export > Create AMT database'' from the main menu bar.
  * In the dialog, enter the following information and click ''Ok''   
      * Click on the ''...'' button to browse to a folder (default folder is the hEIDI project folder) where you want to save the AMT database file and click ''Open''
      * Analysis duration in minutes
      * Analysis delay in minutes
{{:how_to:amtexport_gui.png|}}
  * A confirmation dialog will indicate when saving process is finished.\\
{{:amtexportconfirmdialog.png|}}

===== AMT database model =====

When creating an AMT database (MS Access) from hEIDI, following tables are populated:  

  * **__Table AMT__**: species of the exported User context
    * AMT_ID: index for this AMT tag (generated)
    * AMTMonoisotopicMass: peptide calculated mass
    * NET: computed from peptide (aligned) retention time using the formula: NET = (retentionTimeSeconds/60 - delayMinutes) / durationMinutes
    * PNET: null
    * MSMS_Obs_Count: # of child species
    * High_Normalized_Score: score (max of child peptides scores)
    * High_Discriminant_Score: null
    * Sequence: peptide sequence
    * **NEW** :!: **msidb_peptide_match_id**: peptide_match_id used in MSIdb to create this AMT tag
  * **__Table AMT_Proteins__**: proteins on which species match
    * Protein_ID: protein identifier
    * Protein_name: protein accession
  * **__Table AMT_to_Protein_Map__**: map table between AMT & proteins
  * **__Table protein_group__**: protein groups in which proteins are gathered
    * protein_group_id: protein group identifier
    * master_id: master protein identifier
    * protein_accession: master protein accession
    * score: master protein score
    * nb_amt_match: # of peptides that match on master protein
    * msidb_pg_id: protein group identifier in MSIdb (protein_group table)
  * **__Table protein_to_protein_group_map__**: map table between proteins & protein groups
    * protein_id: protein identifier
    * protein_group_id: protein group identifier
    * nb_amt_match: # of peptides that match on this protein in this protein group
  * **__Table identification__**: identifications used in the exported User context
    * identification_name: names of identifications included in the exported User context
  * **__Table build__**: general information
    * date: AMTdb creation date
    * msidb_name: MSIdb name
    * context_name: name of the exported context
    * context_is_saved: is the exported context has been saved to MSIdb ?
    * msidb_context_id: context identifier in the MSIdb (look at this field only if the context has been saved to MSIdb)
    * **NEW** :!: **duration_minutes**: analysis duration in minutes
    * **NEW** :!: **delay_minutes**: analysis delay in minutes

:!: **Notes**: 
  * UMCs tables were populated using '[[how_to:includeumcinamtdb|Read UMCs]]' tool until hEIDI 1.12.0.\\
  * Since hEIDI 1.13.0, [[how_to:importumctomsidb|UMCs result files are included into MSIdb]] (instead of AMTdb)


{{:how_to:amtexport_relationsmsaccess.png|Relationships in the AMT database (MS Access)}}