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:

• 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.
  

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:

• UMCs tables were populated using 'Read UMCs' tool until hEIDI 1.12.0.
  
• Since hEIDI 1.13.0, UMCs result files are included into MSIdb (instead of AMTdb)