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.
• Browse to a folder where you want to save the AMT database file and click Open.
• A confirmation dialog will indicate when saving process is finished.
  

Note : Before generating a new AMT db from a context, protein grouping should have been executed !

How specific values are calculated:

• MonoistopicMass: calculated_mass
• NET: (Retention Time/60)-5)/80
• 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 AMTdb, the following filters are applied (suppression):

• Reverse proteins
• Species with a sequence < 7
• Proteins identified by only 1 species with a score < 60

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
  • 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)

UMCs tables are populated when using 'Read UMCs' tool.