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--- how_to:generateamtdb [2010/05/28 07:58]
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+++ how_to:generateamtdb [2012/02/29 12:08]
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@@ Line 1: / Line 1: @@
 ====== Generate a new AMT database from a context ======
-To generate a new AMT database in the MS Access format (.mdf file) from a given User context, follow these steps:
+:!: **Requirements** \\
-{{:amtexport_menu.png |Export a context to a new AMT database}}
+  * 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
+\\
+\\
+\\
+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.
-  * Browse to a folder where you want to save the AMT database file and click ''Open''.
+  * 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 filters & Details about some field calculations =====
-\\
-**__Note__** : Before generating a new AMT db from a context, [[how_to:proteingrouping|protein grouping]] should have been executed !
+How specific values are calculated:
-\\
+  * MonoistopicMass: calculated_mass
-\\
+  * NET: (Retention Time/60)-delay)/duration (delay & duration are information entered by user, retention time is expected in seconds)
+  * PNET : null
+  * MS_MS_Obs_Count: # of child species
+  * sequence: species sequence
+  * High_Normalized_Score: score (max of child species scores)
+  * High_Discriminant_Score: null
 ===== 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 = (rtSeconds/60 - delayMinutes) / durationMinutes
+    * PNET:
+    * MSMS_Obs_Count:
+    * High_Normalized_Score: peptide score
+    * High_Discriminant_Score:
+    * Sequence: peptide sequence
+    * 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)
+    * duration_minutes: analysis duration in minutes
+    * 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)
-Below is the AMT database model showing relationships between tables in MS Access.\\
-Only the three tables ''AMT'', ''AMT_Proteins'' and ''AMT_to_Protein_Map'' are populated. The other tables doesn't contain any records. They will be later populated in the AMT pipeline.\\
-  * The ''AMT'' table contains all the peptides of the context.
+{{:how_to:amtexport_relationsmsaccess.png|Relationships in the AMT database (MS Access)}}
-  * The ''AMT Proteins'' table contains all the proteins of the context.
-  * The ''AMT to Protein Map'' table links the two previous tables to indicate by which peptides proteins are identified.
-{{:amtexport_relationsmsaccess.png|Relationships in the AMT database (MS Access)}}

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