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====== Generate a new AMT database from a context ====== | ====== 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 the User context you want to export | ||
* Select ''MS Identifications > Context > Export > Create AMT database'' from the main menu bar. | * 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.\\ | * A confirmation dialog will indicate when saving process is finished.\\ | ||
{{:amtexportconfirmdialog.png|}} | {{:amtexportconfirmdialog.png|}} | ||
- | \\ | + | |
- | \\ | + | |
- | \\ | + | |
- | **__Note__** : Before generating a new AMT db from a context, [[how_to:proteingrouping|protein grouping]] should have been executed ! | + | |
- | \\ | + | |
- | \\ | + | |
===== AMT database model ===== | ===== 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 | ||
- | Below is the AMT database model showing relationships between tables in MS Access.\\ | + | :!: **Notes**: |
- | 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.\\ | + | * 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) | ||
- | * The ''AMT'' table contains all the peptides of the context. | ||
- | * 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. | ||
{{:how_to:amtexport_relationsmsaccess.png|Relationships in the AMT database (MS Access)}} | {{:how_to:amtexport_relationsmsaccess.png|Relationships in the AMT database (MS Access)}} |