how_to:generateamtdb
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how_to:generateamtdb [2010/08/03 09:44] 132.168.74.230 |
how_to:generateamtdb [2012/02/29 12:08] 132.168.73.124 |
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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 filters & Details about some field calculations ===== | ||
| - | Below is the actual AMT database model showing relationships between tables in MS Access.\\ | + | 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 | ||
| - | When exporting an AMT database from hEIDI, 5 tables are populated: | + | ===== AMT database model ===== |
| + | |||
| + | When creating an AMT database (MS Access) from hEIDI, following tables are populated: | ||
| - | * **__Table AMT__** | + | * **__Table AMT__**: species of the exported User context |
| - | * **__Table AMT_Proteins__** | + | * 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_ID: protein identifier | ||
| * Protein_name: protein accession | * Protein_name: protein accession | ||
| - | * **__Table AMT to Protein Map__** | + | * **__Table AMT_to_Protein_Map__**: map table between AMT & proteins |
| - | * **__Table protein_to_protein_group_map__** | + | * **__Table protein_group__**: protein groups in which proteins are gathered |
| - | * 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 protein_group__** | + | |
| * protein_group_id: protein group identifier | * protein_group_id: protein group identifier | ||
| * master_id: master protein identifier | * master_id: master protein identifier | ||
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| * nb_amt_match: # of peptides that match on master protein | * nb_amt_match: # of peptides that match on master protein | ||
| * msidb_pg_id: protein group identifier in MSIdb (protein_group table) | * msidb_pg_id: protein group identifier in MSIdb (protein_group table) | ||
| - | * **__Table identification__** | + | * **__Table protein_to_protein_group_map__**: map table between proteins & protein groups |
| - | * identification_name: names of identifications included in the exported context | + | * protein_id: protein identifier |
| - | * **__Table build__** | + | * 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 | * date: AMTdb creation date | ||
| * msidb_name: MSIdb name | * msidb_name: MSIdb name | ||
| Line 45: | Line 73: | ||
| * context_is_saved: is the exported context has been saved to MSIdb ? | * 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) | * 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) | ||
| + | |||
| - | UMCs tables are populated when using '[[how_to:includeumcinamtdb|Read UMCs]]' tool. | ||
| {{:how_to:amtexport_relationsmsaccess.png|Relationships in the AMT database (MS Access)}} | {{:how_to:amtexport_relationsmsaccess.png|Relationships in the AMT database (MS Access)}} | ||
how_to/generateamtdb.txt · Last modified: 2012/02/29 12:30 by 132.168.73.124
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