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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:

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 !

AMT database filters

How specific values are calculated:

MonoistopicMass: calculated_mass of the species
NET: Median ¹⁾

¹⁾

retention_time/60)-5)/80)

PNET : null
MS_MS_Obs_Count: count(peptide_id) i.e. # of grouped species
High_Normalized_Score: max(score(peptide))

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

===== 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
- 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.

Relationships in the AMT database (MS Access)

hEIDI

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Generate a new AMT database from a context

AMT database filters

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