how_to:generateamtdb
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how_to:generateamtdb [2012/02/29 12:06] 132.168.73.124 |
how_to:generateamtdb [2012/02/29 12:09] 132.168.73.124 |
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| * **[[how_to:alignretentiontime|Retention time alignment]]** & **[[how_to:recomputeretentiontime|retention time recomputing]]** algorithms may have to be run before creating | * **[[how_to:alignretentiontime|Retention time alignment]]** & **[[how_to:recomputeretentiontime|retention time recomputing]]** algorithms may have to be run before creating | ||
| * Save your MSIdb | * Save your MSIdb | ||
| + | \\ | ||
| + | \\ | ||
| + | \\ | ||
| To generate a new AMT database in the MS Access format (.mdb file) from a given User context, follow these steps: | To generate a new AMT database in the MS Access format (.mdb file) from a given User context, follow these steps: | ||
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| * A confirmation dialog will indicate when saving process is finished.\\ | * A confirmation dialog will indicate when saving process is finished.\\ | ||
| {{:amtexportconfirmdialog.png|}} | {{:amtexportconfirmdialog.png|}} | ||
| - | |||
| - | ===== AMT database filters & Details about some field calculations ===== | ||
| - | |||
| - | 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 ===== | ===== AMT database model ===== | ||
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| * AMT_ID: index for this AMT tag (generated) | * AMT_ID: index for this AMT tag (generated) | ||
| * AMTMonoisotopicMass: peptide calculated mass | * AMTMonoisotopicMass: peptide calculated mass | ||
| - | * NET: computed from peptide (aligned) retention time using the formula: NET = (rtSeconds/60 - delayMinutes) / durationMinutes | + | * NET: computed from peptide (aligned) retention time using the formula: NET = (retentionTimeSeconds/60 - delayMinutes) / durationMinutes |
| - | * PNET: | + | * PNET: null |
| - | * MSMS_Obs_Count: | + | * MSMS_Obs_Count: # of child species |
| - | * High_Normalized_Score: peptide score | + | * High_Normalized_Score: score (max of child peptides scores) |
| - | * High_Discriminant_Score: | + | * High_Discriminant_Score: null |
| * Sequence: peptide sequence | * Sequence: peptide sequence | ||
| * msidb_peptide_match_id: peptide_match_id used in MSIdb to create this AMT tag | * msidb_peptide_match_id: peptide_match_id used in MSIdb to create this AMT tag | ||
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| :!: **Notes**: | :!: **Notes**: | ||
| * UMCs tables were populated using '[[how_to:includeumcinamtdb|Read UMCs]]' tool until hEIDI 1.12.0.\\ | * UMCs tables were populated using '[[how_to:includeumcinamtdb|Read UMCs]]' tool until hEIDI 1.12.0.\\ | ||
| - | * Since hEIDI 1.13.0, UMCs result files are included into MSIdb (instead of AMTdb) | + | * 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)}} | {{: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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