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Generate a new AMT database from a context
Requirements
Context have to be grouped previously.
You may want apply some filters during this step:
Notes
Retention time alignment & retention time recomputing algorithms may have to be run before creating
To generate a new AMT database in the MS Access format (.mdf file) from a given User context, follow these steps:
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
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
Below is the actual AMT database model showing relationships between tables in MS Access.
When exporting an AMT database from hEIDI, 5 tables are populated:
Table AMT: species of the exported User context
Table AMT_Proteins: proteins on which species match
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
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
UMCs tables are populated when using 'Read UMCs' tool.