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Generate a new AMT database from a context

:!: Requirements

  • Context have to be 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
  • Retention time alignment & 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:

Export a context to a new AMT database

  • 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

  • A confirmation dialog will indicate when saving process is finished.

AMT database model

When creating an AMT database (MS Access) from hEIDI, following tables are populated:

  • Table AMT: species of the exported User context
    • AMT_ID: index for this AMT tag (generated)
    • AMTMonoisotopicMass: peptide calculated mass
    • NET: computed from peptide (aligned) retention time using the formula: NET = (retentionTimeSeconds/60 - delayMinutes) / durationMinutes
    • PNET: null
    • MSMS_Obs_Count: # of child species
    • High_Normalized_Score: score (max of child peptides scores)
    • High_Discriminant_Score: null
    • Sequence: peptide sequence
    • NEW :!: 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_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)
    • NEW :!: duration_minutes: analysis duration in minutes
    • NEW :!: delay_minutes: analysis delay in minutes

:!: Notes:

Relationships in the AMT database (MS Access)

how_to/generateamtdb.txt · Last modified: 2012/02/29 12:30 by