===== Model D.4 =====

==== List of tables ====

  * [[#admin_infos|admin_infos]]
  * [[#context|context]]
  * [[#context_identification|context_identification]]
  * [[#context_properties|context_properties]]
  * [[#database|database]]
  * [[#description|description]]
  * [[#enzyme|enzyme]]
  * [[#fixed_ptm|fixed_ptm]]
  * [[#fragment_matches|fragment_matches]]
  * [[#identification|identification]]
  * [[#identification_properties|identification_properties]]
  * [[#ion_search|ion_search]]
  * [[#match|match]]
  * [[#msms_search|msms_search]]
  * [[#peptide|peptide]]
  * [[#peptide_children|peptide_children]]
  * [[#peptide_fragmentation|peptide_fragmentation]]
  * [[#peptide_group|peptide_group]]
  * [[#peptide_group_content|peptide_group_content]]
  * [[#peptide_properties|peptide_properties]]
  * [[#peptide_ptm|peptide_ptm]]
  * [[#property|property]]
  * [[#property_group|property_group]]
  * [[#property_group_content|property_group_content]]
  * [[#protein|protein]]
  * [[#protein_group|protein_group]]
  * [[#protein_group_content|protein_group_content]]
  * [[#protein_group_content_match|protein_group_content_match]]
  * [[#protein_group_content_properties|protein_group_content_properties]]
  * [[#protein_group_properties|protein_group_properties]]
  * [[#ptm|ptm]]
  * [[#query|query]]
  * [[#run|run]]
  * [[#run_properties|run_properties]]
  * [[#sample|sample]]
  * [[#search_settings|search_settings]]
  * [[#spectrum|spectrum]]
  * [[#used_enzyme|used_enzyme]]
  * [[#variable_ptm|variable_ptm]]

====== admin_infos ======

===== (Physical Name: admin_infos) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|model_version (PK)|model_version|VARCHAR(50)|PK|NOT NULL|
|creation_date|creation_date|DATE| | |
|update_date|update_date|DATE| | |

====== context ======

===== (Physical Name: context) =====

A context is a set of identifications or a set of children context (context can be organized hierarchically). Peptides and protein sets are associated to context :for this reason, each identification is represented by a context which is the search. Thanks to that, peptide grouping and protein grouping can be stored in this structure because a context defines the identifications that have to be grouped. Context can also be described by a set of properties.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|context_id (PK)|context_id|INTEGER|PK|NOT NULL|
|parent_context_id  ([[#context|FK]])|parent_context_id|INTEGER| |NOT NULL|
|name|name|VARCHAR(50)| | |
| The name of the context ||||
|description|description|VARCHAR(255)| | |
| The description of the context content ||||
|context_type|context_type|VARCHAR(100)| | |
| ID_SEARCH for context representing a unique search or USER for user defined context. ||||

References

  * [[#context|context]] through (parent_context_id)

Referenced By

  * [[#context|context]] referencing (context_id)
  * [[#context_properties|context_properties]] referencing (context_id)
  * [[#context_identification|context_identification]] referencing (context_id)
  * [[#peptide|peptide]] referencing (context_id)
  * [[#protein_group|protein_group]] referencing (context_id)
  * [[#identification|identification]] referencing (context_id)

====== context_identification ======

===== (Physical Name: context_identification) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|context_id (PK)  ([[#context|FK]])|context_id|INTEGER|PK|NOT NULL|
|identification_id (PK)  ([[#identification|FK]])|identification_id|INTEGER|PK|NOT NULL|

References

  * [[#context|context]] through (context_id)
  * [[#identification|identification]] through (identification_id)

====== context_properties ======

===== (Physical Name: context_properties) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|property_group_id (PK)  ([[#property_group|FK]])|property_group_id|INTEGER|PK|NOT NULL|
|context_id (PK)  ([[#context|FK]])|context_id|INTEGER|PK|NOT NULL|

References

  * [[#context|context]] through (context_id)
  * [[#property_group|property_group]] through (property_group_id)

====== database ======

===== (Physical Name: database) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|database_id (PK)|database_id|INTEGER|PK|NOT NULL|
|name|name|VARCHAR(50)| | |
|release|release|VARCHAR(100)| | |
|location|location|VARCHAR(100)| | |
|sequence_count|sequence_count|INTEGER| | |

Referenced By

  * [[#search_settings|search_settings]] referencing (database_id)

====== description ======

===== (Physical Name: description) =====

The description of the identification search.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|description_id (PK)|description_id|INTEGER|PK|NOT NULL|
|user_name|user_name|VARCHAR(50)| | |
| The name of the user who submit the search to the search engine. ||||
|user_email|user_email|VARCHAR(80)| | |
| The email of the user. ||||
|search_date|search_date|DATE| | |
| the date of the search. ||||
|search_title|search_title|VARCHAR(200)| | |
|sourcefile_type|sourcefile_type|VARCHAR(50)| | |
| the type of the source file submitted to the search engine. The sourcefile is the file at the very beginning of the whole search process. This can be a peak list file (MGF, PKL, DTA, mzXML, etc) or a raw data file if the search process is done via Mascot Daemon for example (.raw, .wiff, etc) ||||
|sourcefile_url|sourcefile_url|VARCHAR(200)| | |
| the path to the source file if exists. ||||
|search_settings_id  ([[#search_settings|FK]])|search_settings_id|INTEGER| |NOT NULL|

References

  * [[#search_settings|search_settings]] through (search_settings_id)

Referenced By

  * [[#identification|identification]] referencing (description_id)

====== enzyme ======

===== (Physical Name: enzyme) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|name (PK)|name|VARCHAR(50)|PK|NOT NULL|

Referenced By

  * [[#used_enzyme|used_enzyme]] referencing (name)

====== fixed_ptm ======

===== (Physical Name: fixed_ptm) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|ptm_name (PK)  ([[#ptm|FK]])|ptm_name|VARCHAR(50)|PK|NOT NULL|
|search_settings_id (PK)  ([[#search_settings|FK]])|search_settings_id|INTEGER|PK|NOT NULL|
|ptm_index|ptm_index|INTEGER| | |
|ptm_type|ptm_type|VARCHAR(50)| | |

References

  * [[#search_settings|search_settings]] through (search_settings_id)
  * [[#ptm|ptm]] through (ptm_name)

====== fragment_matches ======

===== (Physical Name: fragment_matches) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|fragment_matches_id (PK)|fragment_matches_id|INTEGER|PK|NOT NULL|
|matches_count|matches_count|INTEGER| | |
|used_peaks_count|used_peaks_count|INTEGER| | |
|content|content|[-2]| | |

Referenced By

  * [[#peptide|peptide]] referencing (fragment_matches_id)

Content Example 

This is an [[:userguide:FragmentMatchesContent|example of the content column]]. This column contains the fragment matching of the associated peptide, serialized in XML.   

====== identification ======

===== (Physical Name: identification) =====

An identification search performed with a search engine such as Mascot.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|identification_id (PK)|identification_id|INTEGER|PK|NOT NULL|
|description_id  ([[#description|FK]])|description_id|INTEGER| |NOT NULL|
|resultfile_url|resultfile_url|VARCHAR(200)| | |
| The file containing the raw identification result produced by the search engine. ||||
|queries_count|queries_count|INTEGER| | |
| The number of queries actually associated to this identification in the database ||||
|submitted_queries_count|submitted_queries_count|INTEGER| | |
| The number of spectra submitted to the search engine. This count may be different from the number of queries actually associated to this identification in the database (queries_count) since only queries providing peptide identification are stored in the database. ||||
|search_context_id  ([[#context|FK]])|search_context_id|INTEGER| |NOT NULL|

References

  * [[#context|context]] through (search_context_id)
  * [[#description|description]] through (description_id)

Referenced By

  * [[#context_identification|context_identification]] referencing (identification_id)
  * [[#identification_properties|identification_properties]] referencing (identification_id)
  * [[#query|query]] referencing (identification_id)
  * [[#run|run]] referencing (identification_id)

====== identification_properties ======

===== (Physical Name: identification_properties) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|property_group_id (PK)  ([[#property_group|FK]])|property_group_id|INTEGER|PK|NOT NULL|
|identification_id (PK)  ([[#identification|FK]])|identification_id|INTEGER|PK|NOT NULL|

References

  * [[#identification|identification]] through (identification_id)
  * [[#property_group|property_group]] through (property_group_id)

====== ion_search ======

===== (Physical Name: ion_search) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|search_settings_id (PK)  ([[#search_settings|FK]])|search_settings_id|INTEGER|PK|NOT NULL|
|max_protein_mass|max_protein_mass|DOUBLE| | |
|min_protein_mass|min_protein_mass|DOUBLE| | |
|protein_pi|protein_pi|DOUBLE| | |

References

  * [[#search_settings|search_settings]] through (search_settings_id)

====== match ======

===== (Physical Name: match) =====

A match between a peptide and a protein.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|match_id (PK)|match_id|INTEGER|PK|NOT NULL|
|protein_accession  ([[#protein|FK]])|protein_accession|VARCHAR(50)| |NOT NULL|
|peptide_id  ([[#peptide|FK]])|peptide_id|INTEGER| |NOT NULL|
|start|start|INTEGER| | |
| The start position of the peptide on the protein ||||
|stop|stop|INTEGER| | |
| The stop position of the peptide on the protein ||||
|score|score|DOUBLE| | |
| The score of the peptide for this unique protein. For some unknown reasons, MASCOT for example provides a different score for each protein this peptide matches to. ||||
|state|state|VARCHAR(50)| | |
| relevant or duplicated ||||

References

  * [[#protein|protein]] through (protein_accession)
  * [[#peptide|peptide]] through (peptide_id)

Referenced By

  * [[#protein_group_content_match|protein_group_content_match]] referencing (match_id)

====== msms_search ======

===== (Physical Name: msms_search) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|search_settings_id (PK)  ([[#search_settings|FK]])|search_settings_id|INTEGER|PK|NOT NULL|
|fragment_error_tolerance|fragment_error_tolerance|DOUBLE| | |
|fragment_error_tolerance_unit|fragment_error_tolerance_unit|VARCHAR(50)| | |

References

  * [[#search_settings|search_settings]] through (search_settings_id)

====== peptide ======

===== (Physical Name: peptide) =====

A peptide is an amino acid (AA) sequence identified from an MSMS experiment. A peptide can be an AA sequence that potentially match a fragmentation spectrum (called observed peptide, cause they are experimentally "observed" through their fragmentation spectrum) or a group of observed peptides sharing the same caracteristics. In this later case, the observed peptides are called children peptides.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|peptide_id (PK)|peptide_id|INTEGER|PK|NOT NULL|
|charge|charge|INTEGER| | |
| the charge state of the peptide ||||
|missed_cleavage|missed_cleavage|INTEGER| | |
| Number of missed cleavages in the peptide sequence ||||
|calculated_mass|calculated_mass|DOUBLE| | |
| The mass calculated from the AA sequence, taking modifications into account. ||||
|experimental_mass|experimental_mass|DOUBLE| | |
| The experimental mass of this peptide. For peptide observed from a spectrum, this value is the same as the spectrum ion_parent_mass, but for peptides having children, this can be a value computed mass (for exemple the mean) from all observed spectra experimental masses. ||||
|ion_parent_intensity|ion_parent_intensity|DOUBLE| | |
| The intensity of the precursor for this peptide eventually recalculated from the XIC, or calculated from children observed peptides. ||||
|retention_time|retention_time|DOUBLE| | |
| The elution time of this peptide eventually refined from XIC or calculated from children observed peptides. ||||
|sequence|sequence|VARCHAR(0)| |NOT NULL|
| The AA sequence of this peptide ||||
|context_id  ([[#context|FK]])|context_id|INTEGER| |NOT NULL|
|score|score|DOUBLE| | |
| The score assigned by the search engine to this peptide. ||||
|original_rank|original_rank|INTEGER| | |
| the rank of this peptide. Search engines usually provides many peptides per spectrum and rank this peptides according to their score. This value is the rank originally provided by the search engine. ||||
|query_id  ([[#query|FK]])|query_id|INTEGER| |NOT NULL|
|fragment_matches_id  ([[#fragment_matches|FK]])|fragment_matches_id|INTEGER| |NOT NULL|
|peptide_fragmentation_id  ([[#peptide_fragmentation|FK]])|peptide_fragmentation_id|INTEGER| |NOT NULL|

References

  * [[#query|query]] through (query_id)
  * [[#peptide_fragmentation|peptide_fragmentation]] through (peptide_fragmentation_id)
  * [[#context|context]] through (context_id)
  * [[#fragment_matches|fragment_matches]] through (fragment_matches_id)

Referenced By

  * [[#match|match]] referencing (peptide_id)
  * [[#peptide_children|peptide_children]] referencing (peptide_id)
  * [[#peptide_children|peptide_children]] referencing (peptide_id)
  * [[#peptide_group_content|peptide_group_content]] referencing (peptide_id)
  * [[#peptide_ptm|peptide_ptm]] referencing (peptide_id)
  * [[#peptide_properties|peptide_properties]] referencing (peptide_id)

====== peptide_children ======

===== (Physical Name: peptide_children) =====

Parent-child relationship between peptides. See peptide description.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|parent_peptide_id (PK)  ([[#peptide|FK]])|parent_peptide_id|INTEGER|PK|NOT NULL|
|child_peptide_id (PK)  ([[#peptide|FK]])|child_peptide_id|INTEGER|PK|NOT NULL|

References

  * [[#peptide|peptide]] through (child_peptide_id)
  * [[#peptide|peptide]] through (parent_peptide_id)

====== peptide_fragmentation ======

===== (Physical Name: peptide_fragmentation) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|peptide_fragmentation_id (PK)|peptide_fragmentation_id|INTEGER|PK|NOT NULL|
|fragments_count|fragments_count|INTEGER| | |
|content|content|[-2]| | |

Referenced By

  * [[#peptide|peptide]] referencing (peptide_fragmentation_id)

Content Example 

This is an [[:userguide:FragmentationContent|example of the content column]]. This column contains the theoretical fragmentation of the associated peptide, serialized in XML.    

====== peptide_group ======

===== (Physical Name: peptide_group) =====

Identifies a set of peptides belonging to one or more proteins.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|peptide_group_id (PK)|peptide_group_id|INTEGER|PK|NOT NULL|

Referenced By

  * [[#peptide_group_content|peptide_group_content]] referencing (peptide_group_id)
  * [[#protein_group_content|protein_group_content]] referencing (peptide_group_id)

====== peptide_group_content ======

===== (Physical Name: peptide_group_content) =====

The content of a set of peptides (multiple records lists the peptides belonging to a peptide_group)

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|peptide_group_id (PK)  ([[#peptide_group|FK]])|peptide_group_id|INTEGER|PK|NOT NULL|
|peptide_id (PK)  ([[#peptide|FK]])|peptide_id|INTEGER|PK|NOT NULL|

References

  * [[#peptide_group|peptide_group]] through (peptide_group_id)
  * [[#peptide|peptide]] through (peptide_id)

====== peptide_properties ======

===== (Physical Name: peptide_properties) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|property_group_id (PK)  ([[#property_group|FK]])|property_group_id|INTEGER|PK|NOT NULL|
|peptide_id (PK)  ([[#peptide|FK]])|peptide_id|INTEGER|PK|NOT NULL|

References

  * [[#peptide|peptide]] through (peptide_id)
  * [[#property_group|property_group]] through (property_group_id)

====== peptide_ptm ======

===== (Physical Name: peptide_ptm) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|id (PK)|id|INTEGER|PK|NOT NULL|
|ptm_name  ([[#ptm|FK]])|ptm_name|VARCHAR(50)| |NOT NULL|
|peptide_id  ([[#peptide|FK]])|peptide_id|INTEGER| |NOT NULL|
|location|location|INTEGER| | |

References

  * [[#peptide|peptide]] through (peptide_id)
  * [[#ptm|ptm]] through (ptm_name)

====== property ======

===== (Physical Name: property) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|property_id (PK)|property_id|INTEGER|PK|NOT NULL|
|a_key|a_key|VARCHAR(100)| | |
|a_value|a_value|VARCHAR(100)| | |
|a_type|a_type|VARCHAR(50)| | |
|group_value  ([[#property_group|FK]])|group_value|INTEGER| |NOT NULL|
|description|description|VARCHAR(255)| | |

References

  * [[#property_group|property_group]] through (group_value)

Referenced By

  * [[#property_group_content|property_group_content]] referencing (property_id)

====== property_group ======

===== (Physical Name: property_group) =====

A set of properties associated to an object (identification, context, peptide, etc). For example, the filter values used to validate the identification result, the values used to generate the result, or statistical values calculated from the identification result.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|property_group_id (PK)|property_group_id|INTEGER|PK|NOT NULL|
|name|name|VARCHAR(150)| |NOT NULL|
| The name of the set. ||||
|description|description|VARCHAR(255)| | |
| A short description of the set of properties. ||||

Referenced By

  * [[#context_properties|context_properties]] referencing (property_group_id)
  * [[#identification_properties|identification_properties]] referencing (property_group_id)
  * [[#property|property]] referencing (property_group_id)
  * [[#protein_group_content_properties|protein_group_content_properties]] referencing (property_group_id)
  * [[#protein_group_properties|protein_group_properties]] referencing (property_group_id)
  * [[#run_properties|run_properties]] referencing (property_group_id)
  * [[#property_group_content|property_group_content]] referencing (property_group_id)
  * [[#peptide_properties|peptide_properties]] referencing (property_group_id)

====== property_group_content ======

===== (Physical Name: property_group_content) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|property_id (PK)  ([[#property|FK]])|property_id|INTEGER|PK|NOT NULL|
|property_group_id (PK)  ([[#property_group|FK]])|property_group_id|INTEGER|PK|NOT NULL|

References

  * [[#property|property]] through (property_id)
  * [[#property_group|property_group]] through (property_group_id)

====== protein ======

===== (Physical Name: protein) =====

An entry in a protein databse identified by an accession number.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|accession (PK)|accession|VARCHAR(50)|PK|NOT NULL|
| The label used by the search engine to identify the protein. ||||
|description|description|VARCHAR(1024)| | |
| The description of the protein. ||||
|length|length|INTEGER| | |
| The length of the protein. ||||
|mass|mass|DOUBLE| | |
| The molecular mass of the protein. ||||
|pi|pi|DOUBLE| | |
| The isoelectric point of the protein. ||||
|sequence|sequence|CLOB| | |
| The amino acid sequence of the protein. ||||

Referenced By

  * [[#protein_group_content|protein_group_content]] referencing (accession)
  * [[#match|match]] referencing (accession)

====== protein_group ======

===== (Physical Name: protein_group) =====

Identifies a set of one or more proteins

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|protein_group_id (PK)|protein_group_id|INTEGER|PK|NOT NULL|
|context_id  ([[#context|FK]])|context_id|INTEGER| |NOT NULL|
|validation_mask|validation_mask|INTEGER| | |

References

  * [[#context|context]] through (context_id)

Referenced By

  * [[#protein_group_content|protein_group_content]] referencing (protein_group_id)
  * [[#protein_group_properties|protein_group_properties]] referencing (protein_group_id)

====== protein_group_content ======

===== (Physical Name: protein_group_content) =====

The content of a protein group (multiple records lists the proteins belonging to a protein_group and the set of peptides that identify these proteins)

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|protein_group_content_id (PK)|protein_group_content_id|INTEGER|PK|NOT NULL|
|protein_group_id  ([[#protein_group|FK]])|protein_group_id|INTEGER| |NOT NULL|
|protein_accession  ([[#protein|FK]])|protein_accession|VARCHAR(50)| |NOT NULL|
|validation_mask|validation_mask|INTEGER| | |
|score|score|DOUBLE| | |
| The identification score of the protein. ||||
|coverage|coverage|DOUBLE| | |
| The percentage of the protein's sequence covered by the set of peptides. ||||
|is_master|is_master|BOOLEAN| | |
| True if the protein can be considered as "typical" of the set it belongs to. This is for example the protein displayed by the search engine in order to "summarize" the results. ||||
|match_count|match_count|INTEGER| | |
| The number of peptides in the peptide set ||||
|peptide_group_id  ([[#peptide_group|FK]])|peptide_group_id|INTEGER| |NOT NULL|

References

  * [[#protein|protein]] through (protein_accession)
  * [[#peptide_group|peptide_group]] through (peptide_group_id)
  * [[#protein_group|protein_group]] through (protein_group_id)

Referenced By

  * [[#protein_group_content_properties|protein_group_content_properties]] referencing (protein_group_content_id)
  * [[#protein_group_content_match|protein_group_content_match]] referencing (protein_group_content_id)

====== protein_group_content_match ======

===== (Physical Name: protein_group_content_match) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|protein_group_content_id (PK)  ([[#protein_group_content|FK]])|protein_group_content_id|INTEGER|PK|NOT NULL|
|match_id (PK)  ([[#match|FK]])|match_id|INTEGER|PK|NOT NULL|

References

  * [[#protein_group_content|protein_group_content]] through (protein_group_content_id)
  * [[#match|match]] through (match_id)

====== protein_group_content_properties ======

===== (Physical Name: protein_group_content_properties) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|property_group_id (PK)  ([[#property_group|FK]])|property_group_id|INTEGER|PK|NOT NULL|
|protein_group_content_id (PK)  ([[#protein_group_content|FK]])|protein_group_content_id|INTEGER|PK|NOT NULL|

References

  * [[#protein_group_content|protein_group_content]] through (protein_group_content_id)
  * [[#property_group|property_group]] through (property_group_id)

====== protein_group_properties ======

===== (Physical Name: protein_group_properties) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|property_group_id (PK)  ([[#property_group|FK]])|property_group_id|INTEGER|PK|NOT NULL|
|protein_group_id (PK)  ([[#protein_group|FK]])|protein_group_id|INTEGER|PK|NOT NULL|

References

  * [[#protein_group|protein_group]] through (protein_group_id)
  * [[#property_group|property_group]] through (property_group_id)

====== ptm ======

===== (Physical Name: ptm) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|name (PK)|name|VARCHAR(50)|PK|NOT NULL|

Referenced By

  * [[#fixed_ptm|fixed_ptm]] referencing (name)
  * [[#peptide_ptm|peptide_ptm]] referencing (name)
  * [[#variable_ptm|variable_ptm]] referencing (name)

====== query ======

===== (Physical Name: query) =====

One of the queries submitted to the search engine. A query represents a spectrum contained in the submitted peaklist. Search engines such as MASCOT usually identify each spectrum with it's own id and generates a description from some properties of the original spectrum. This table is where these id and description are stored.

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|query_id (PK)|query_id|INTEGER|PK|NOT NULL|
|original_query_id|original_query_id|INTEGER| |NOT NULL|
| The id associated to this query by the search engine. ||||
|identification_id  ([[#identification|FK]])|identification_id|INTEGER| |NOT NULL|
|spectrum_id  ([[#spectrum|FK]])|spectrum_id|INTEGER| |NOT NULL|
|description|description|VARCHAR(1024)| | |
| The description associated to this query by the search engine. ||||

References

  * [[#identification|identification]] through (identification_id)
  * [[#spectrum|spectrum]] through (spectrum_id)

Referenced By

  * [[#peptide|peptide]] referencing (query_id)

====== run ======

===== (Physical Name: run) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|run_id (PK)|run_id|INTEGER|PK|NOT NULL|
|identification_id  ([[#identification|FK]])|identification_id|INTEGER| |NOT NULL|
|run_owner|run_owner|VARCHAR(50)| | |
|analyst|analyst|VARCHAR(50)| | |
|raw_filename|raw_filename|VARCHAR(255)| | |
|spectrometer_type|spectrometer_type|VARCHAR(30)| | |
|spectrometer_name|spectrometer_name|VARCHAR(20)| | |
|lc_method|lc_method|VARCHAR(50)| | |
|ms_method|ms_method|VARCHAR(50)| | |
|run_date|run_date|DATE| | |
|duration|duration|INTEGER| | |
|run_start|run_start|INTEGER| | |
|run_stop|run_stop|INTEGER| | |
|sample_name  ([[#sample|FK]])|sample_name|VARCHAR(50)| |NOT NULL|

References

  * [[#sample|sample]] through (sample_name)
  * [[#identification|identification]] through (identification_id)

Referenced By

  * [[#run_properties|run_properties]] referencing (run_id)

====== run_properties ======

===== (Physical Name: run_properties) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|property_group_id (PK)  ([[#property_group|FK]])|property_group_id|INTEGER|PK|NOT NULL|
|run_id (PK)  ([[#run|FK]])|run_id|INTEGER|PK|NOT NULL|

References

  * [[#property_group|property_group]] through (property_group_id)
  * [[#run|run]] through (run_id)

====== sample ======

===== (Physical Name: sample) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|sample_name (PK)|sample_name|VARCHAR(50)|PK|NOT NULL|
|project_name|project_name|VARCHAR(50)| | |
|study_name|study_name|VARCHAR(50)| | |

Referenced By

  * [[#run|run]] referencing (sample_name)

====== search_settings ======

===== (Physical Name: search_settings) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|search_settings_id (PK)|search_settings_id|INTEGER|PK|NOT NULL|
|software_name|software_name|VARCHAR(50)| | |
|software_version|software_version|VARCHAR(50)| | |
|database_id  ([[#database|FK]])|database_id|INTEGER| |NOT NULL|
|taxonomy|taxonomy|VARCHAR(50)| | |
|searched_seq_count|searched_seq_count|INTEGER| | |
|max_missed_cleavages|max_missed_cleavages|INTEGER| | |
|peptide_mass_error_tolerance|peptide_mass_error_tolerance|DOUBLE| | |
|peptide_mass_error_tolerance_unit|peptide_mass_error_tolerance_unit|VARCHAR(50)| | |
|quantitation|quantitation|VARCHAR(50)| | |

References

  * [[#database|database]] through (database_id)

Referenced By

  * [[#variable_ptm|variable_ptm]] referencing (search_settings_id)
  * [[#msms_search|msms_search]] referencing (search_settings_id)
  * [[#used_enzyme|used_enzyme]] referencing (search_settings_id)
  * [[#fixed_ptm|fixed_ptm]] referencing (search_settings_id)
  * [[#ion_search|ion_search]] referencing (search_settings_id)
  * [[#description|description]] referencing (search_settings_id)

====== spectrum ======

===== (Physical Name: spectrum) =====

The fragmentation spectrum submitted to the search engine

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|spectrum_id (PK)|spectrum_id|INTEGER|PK|NOT NULL|
|initial_id|initial_id|INTEGER| |NOT NULL|
| JE NE SAIS PLUS .... ||||
|ion_parent_mass|ion_parent_mass|DOUBLE| |NOT NULL|
| The precursor m/z. ||||
|ion_parent_intensity|ion_parent_intensity|DOUBLE| | |
| The intensity of the precursor as registered in the peak list (if any). ||||
|retention_time|retention_time|DOUBLE| | |
| The chromatographic time at which this spectrum has been acquired. ||||
|charge|charge|INTEGER| | |
| The charge state of the fragmented ion. ||||
|masses|masses|[-2]| | |
|intensities|intensities|[-2]| | |
|peaks_count|peaks_count|INTEGER| | |

Referenced By

  * [[#query|query]] referencing (spectrum_id)

====== used_enzyme ======

===== (Physical Name: used_enzyme) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|enzyme_name (PK)  ([[#enzyme|FK]])|enzyme_name|VARCHAR(50)|PK|NOT NULL|
|search_settings_id (PK)  ([[#search_settings|FK]])|search_settings_id|INTEGER|PK|NOT NULL|

References

  * [[#search_settings|search_settings]] through (search_settings_id)
  * [[#enzyme|enzyme]] through (enzyme_name)

====== variable_ptm ======

===== (Physical Name: variable_ptm) =====

|Logical Column Name|Physical Column Name|Type|PK|Nullable|
|ptm_name (PK)  ([[#ptm|FK]])|ptm_name|VARCHAR(50)|PK|NOT NULL|
|search_settings_id (PK)  ([[#search_settings|FK]])|search_settings_id|INTEGER|PK|NOT NULL|
|ptm_index|ptm_index|INTEGER| | |
|ptm_type|ptm_type|VARCHAR(50)| | |

References

  * [[#search_settings|search_settings]] through (search_settings_id)
  * [[#ptm|ptm]] through (ptm_name)