userguide:msidbmodeld.3-desc
Table of Contents
MSIdb version D.3
List of tables
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 |
admin_infos_1
(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 (FK) | parent_context_id | INTEGER | ||
| 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 through (parent_context_id)
Referenced By
- context referencing (context_id)
- context_identification referencing (context_id)
- context_properties referencing (context_id)
- identification referencing (context_id)
- peptide referencing (context_id)
- protein_group referencing (context_id)
context_1
(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 (FK) | parent_context_id | INTEGER | ||
| 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_1 through (parent_context_id)
Referenced By
- context_1 referencing (context_id)
- context_properties_1 referencing (context_id)
- identification_1 referencing (context_id)
- peptide_1 referencing (context_id)
- protein_group_1 referencing (context_id)
- context_identification_1 referencing (context_id)
context_identification
(Physical Name: context_identification)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| context_id (PK) (FK) | context_id | INTEGER | PK | NOT NULL |
| identification_id (PK) (FK) | identification_id | INTEGER | PK | NOT NULL |
References
- context through (context_id)
- identification through (identification_id)
context_identification_1
(Physical Name: context_identification)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| context_id (PK) (FK) | context_id | INTEGER | PK | NOT NULL |
| identification_id (PK) (FK) | identification_id | INTEGER | PK | NOT NULL |
References
- identification_1 through (identification_id)
- context_1 through (context_id)
context_properties
(Physical Name: context_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| context_id (PK) (FK) | context_id | INTEGER | PK | NOT NULL |
References
- context through (context_id)
- property_group through (property_group_id)
context_properties_1
(Physical Name: context_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| context_id (PK) (FK) | context_id | INTEGER | PK | NOT NULL |
References
- property_group_1 through (property_group_id)
- context_1 through (context_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 referencing (database_id)
database_1
(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_1 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 (FK) | search_settings_id | INTEGER | ||
References
- search_settings through (search_settings_id)
Referenced By
- identification referencing (description_id)
description_1
(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 (FK) | search_settings_id | INTEGER | ||
References
- search_settings_1 through (search_settings_id)
Referenced By
- identification_1 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 referencing (name)
enzyme_1
(Physical Name: enzyme)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| name (PK) | name | VARCHAR(50) | PK | NOT NULL |
Referenced By
- used_enzyme_1 referencing (name)
fixed_ptm
(Physical Name: fixed_ptm)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| ptm_name (PK) (FK) | ptm_name | VARCHAR(50) | PK | NOT NULL |
| search_settings_id (PK) (FK) | search_settings_id | INTEGER | PK | NOT NULL |
| ptm_index | ptm_index | INTEGER | ||
| ptm_type | ptm_type | VARCHAR(50) |
References
- ptm through (ptm_name)
- search_settings through (search_settings_id)
fixed_ptm_1
(Physical Name: fixed_ptm)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| ptm_name (PK) (FK) | ptm_name | VARCHAR(50) | PK | NOT NULL |
| search_settings_id (PK) (FK) | search_settings_id | INTEGER | PK | NOT NULL |
| ptm_index | ptm_index | INTEGER | ||
| ptm_type | ptm_type | VARCHAR(50) |
References
- search_settings_1 through (search_settings_id)
- ptm_1 through (ptm_name)
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 (FK) | description_id | INTEGER | ||
| 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 (FK) | search_context_id | INTEGER | NOT NULL | |
References
- context through (search_context_id)
- description through (description_id)
Referenced By
- context_identification referencing (identification_id)
- identification_properties referencing (identification_id)
- query referencing (identification_id)
- run referencing (identification_id)
identification_1
(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 (FK) | description_id | INTEGER | ||
| 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 (FK) | search_context_id | INTEGER | NOT NULL | |
References
- description_1 through (description_id)
- context_1 through (search_context_id)
Referenced By
- identification_properties_1 referencing (identification_id)
- query_1 referencing (identification_id)
- run_1 referencing (identification_id)
- context_identification_1 referencing (identification_id)
identification_properties
(Physical Name: identification_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| identification_id (PK) (FK) | identification_id | INTEGER | PK | NOT NULL |
References
- identification through (identification_id)
- property_group through (property_group_id)
identification_properties_1
(Physical Name: identification_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| identification_id (PK) (FK) | identification_id | INTEGER | PK | NOT NULL |
References
- property_group_1 through (property_group_id)
- identification_1 through (identification_id)
ion_search
(Physical Name: ion_search)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| search_settings_id (PK) (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 through (search_settings_id)
ion_search_1
(Physical Name: ion_search)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| search_settings_id (PK) (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_1 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 (FK) | protein_accession | VARCHAR(50) | NOT NULL | |
| peptide_id (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
Referenced By
- protein_group_content_match referencing (match_id)
match_1
(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 (FK) | protein_accession | VARCHAR(50) | NOT NULL | |
| peptide_id (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
Referenced By
- protein_group_content_match_1 referencing (match_id)
msms_search
(Physical Name: msms_search)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| search_settings_id (PK) (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 through (search_settings_id)
msms_search_1
(Physical Name: msms_search)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| search_settings_id (PK) (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_1 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(2147483647) | ||
| The AA sequence of this peptide | ||||
| context_id (FK) | context_id | INTEGER | ||
| 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 (FK) | query_id | INTEGER | ||
References
Referenced By
- match referencing (peptide_id)
- peptide_children referencing (peptide_id)
- peptide_children referencing (peptide_id)
- peptide_group_content referencing (peptide_id)
- peptide_properties referencing (peptide_id)
- peptide_ptm referencing (peptide_id)
peptide_1
(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(2147483647) | ||
| The AA sequence of this peptide | ||||
| context_id (FK) | context_id | INTEGER | ||
| 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 (FK) | query_id | INTEGER | ||
References
Referenced By
- match_1 referencing (peptide_id)
- peptide_children_1 referencing (peptide_id)
- peptide_children_1 referencing (peptide_id)
- peptide_group_content_1 referencing (peptide_id)
- peptide_ptm_1 referencing (peptide_id)
- peptide_properties_1 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) (FK) | parent_peptide_id | INTEGER | PK | NOT NULL |
| child_peptide_id (PK) (FK) | child_peptide_id | INTEGER | PK | NOT NULL |
References
peptide_children_1
(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) (FK) | parent_peptide_id | INTEGER | PK | NOT NULL |
| child_peptide_id (PK) (FK) | child_peptide_id | INTEGER | PK | NOT NULL |
References
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 referencing (peptide_group_id)
- protein_group_content referencing (peptide_group_id)
peptide_group_1
(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_1 referencing (peptide_group_id)
- protein_group_content_1 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) (FK) | peptide_group_id | INTEGER | PK | NOT NULL |
| peptide_id (PK) (FK) | peptide_id | INTEGER | PK | NOT NULL |
References
- peptide through (peptide_id)
- peptide_group through (peptide_group_id)
peptide_group_content_1
(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) (FK) | peptide_group_id | INTEGER | PK | NOT NULL |
| peptide_id (PK) (FK) | peptide_id | INTEGER | PK | NOT NULL |
References
- peptide_group_1 through (peptide_group_id)
- peptide_1 through (peptide_id)
peptide_properties
(Physical Name: peptide_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| peptide_id (PK) (FK) | peptide_id | INTEGER | PK | NOT NULL |
References
- peptide through (peptide_id)
- property_group through (property_group_id)
peptide_properties_1
(Physical Name: peptide_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| peptide_id (PK) (FK) | peptide_id | INTEGER | PK | NOT NULL |
References
- property_group_1 through (property_group_id)
- peptide_1 through (peptide_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 (FK) | ptm_name | VARCHAR(50) | NOT NULL | |
| peptide_id (FK) | peptide_id | INTEGER | NOT NULL | |
| location | location | INTEGER |
References
peptide_ptm_1
(Physical Name: peptide_ptm)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| id (PK) | id | INTEGER | PK | NOT NULL |
| ptm_name (FK) | ptm_name | VARCHAR(50) | NOT NULL | |
| peptide_id (FK) | peptide_id | INTEGER | NOT NULL | |
| location | location | INTEGER |
References
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 (FK) | group_value | INTEGER | ||
| description | description | VARCHAR(255) |
References
- property_group through (group_value)
Referenced By
- property_group_content referencing (property_id)
property_1
(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 (FK) | group_value | INTEGER | ||
| description | description | VARCHAR(255) |
References
- property_group_1 through (group_value)
Referenced By
- property_group_content_1 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(50) | NOT NULL | |
| The name of the set. | ||||
| description | description | VARCHAR(255) | ||
| A short description of the set of properties. | ||||
Referenced By
- context_properties referencing (property_group_id)
- identification_properties referencing (property_group_id)
- peptide_properties referencing (property_group_id)
- property referencing (property_group_id)
- property_group_content referencing (property_group_id)
- protein_group_content_properties referencing (property_group_id)
- protein_group_properties referencing (property_group_id)
- run_properties referencing (property_group_id)
property_group_1
(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(50) | NOT NULL | |
| The name of the set. | ||||
| description | description | VARCHAR(255) | ||
| A short description of the set of properties. | ||||
Referenced By
- identification_properties_1 referencing (property_group_id)
- protein_group_content_properties_1 referencing (property_group_id)
- run_properties_1 referencing (property_group_id)
- peptide_properties_1 referencing (property_group_id)
- context_properties_1 referencing (property_group_id)
- property_group_content_1 referencing (property_group_id)
- property_1 referencing (property_group_id)
- protein_group_properties_1 referencing (property_group_id)
property_group_content
(Physical Name: property_group_content)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_id (PK) (FK) | property_id | INTEGER | PK | NOT NULL |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
References
- property through (property_id)
- property_group through (property_group_id)
property_group_content_1
(Physical Name: property_group_content)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_id (PK) (FK) | property_id | INTEGER | PK | NOT NULL |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
References
- property_group_1 through (property_group_id)
- property_1 through (property_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 | VARCHAR(2147483647) | ||
| The amino acid sequence of the protein. | ||||
Referenced By
- match referencing (accession)
- protein_group_content referencing (accession)
protein_1
(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 | VARCHAR(2147483647) | ||
| The amino acid sequence of the protein. | ||||
Referenced By
- match_1 referencing (accession)
- protein_group_content_1 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 (FK) | context_id | INTEGER | ||
| validation_mask | validation_mask | INTEGER |
References
- context through (context_id)
Referenced By
- protein_group_content referencing (protein_group_id)
- protein_group_properties referencing (protein_group_id)
protein_group_1
(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 (FK) | context_id | INTEGER | ||
| validation_mask | validation_mask | INTEGER |
References
- context_1 through (context_id)
Referenced By
- protein_group_content_1 referencing (protein_group_id)
- protein_group_properties_1 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 (FK) | protein_group_id | INTEGER | NOT NULL | |
| protein_accession (FK) | protein_accession | VARCHAR(50) | NOT NULL | |
| 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 (FK) | peptide_group_id | INTEGER | ||
| validation_mask | validation_mask | INTEGER | ||
References
- peptide_group through (peptide_group_id)
- protein through (protein_accession)
- protein_group through (protein_group_id)
Referenced By
- protein_group_content_match referencing (protein_group_content_id)
- protein_group_content_properties referencing (protein_group_content_id)
protein_group_content_1
(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 (FK) | protein_group_id | INTEGER | NOT NULL | |
| protein_accession (FK) | protein_accession | VARCHAR(50) | NOT NULL | |
| 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 (FK) | peptide_group_id | INTEGER | ||
| validation_mask | validation_mask | INTEGER | ||
References
- protein_1 through (protein_accession)
- peptide_group_1 through (peptide_group_id)
- protein_group_1 through (protein_group_id)
Referenced By
- protein_group_content_match_1 referencing (protein_group_content_id)
- protein_group_content_properties_1 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) (FK) | protein_group_content_id | INTEGER | PK | NOT NULL |
| match_id (PK) (FK) | match_id | INTEGER | PK | NOT NULL |
References
- match through (match_id)
- protein_group_content through (protein_group_content_id)
protein_group_content_match_1
(Physical Name: protein_group_content_match)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| protein_group_content_id (PK) (FK) | protein_group_content_id | INTEGER | PK | NOT NULL |
| match_id (PK) (FK) | match_id | INTEGER | PK | NOT NULL |
References
- match_1 through (match_id)
- protein_group_content_1 through (protein_group_content_id)
protein_group_content_properties
(Physical Name: protein_group_content_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| protein_group_content_id (PK) (FK) | protein_group_content_id | INTEGER | PK | NOT NULL |
References
- property_group through (property_group_id)
- protein_group_content through (protein_group_content_id)
protein_group_content_properties_1
(Physical Name: protein_group_content_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| protein_group_content_id (PK) (FK) | protein_group_content_id | INTEGER | PK | NOT NULL |
References
- protein_group_content_1 through (protein_group_content_id)
- property_group_1 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) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| protein_group_id (PK) (FK) | protein_group_id | INTEGER | PK | NOT NULL |
References
- property_group through (property_group_id)
- protein_group through (protein_group_id)
protein_group_properties_1
(Physical Name: protein_group_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| protein_group_id (PK) (FK) | protein_group_id | INTEGER | PK | NOT NULL |
References
- property_group_1 through (property_group_id)
- protein_group_1 through (protein_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 referencing (name)
- peptide_ptm referencing (name)
- variable_ptm referencing (name)
ptm_1
(Physical Name: ptm)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| name (PK) | name | VARCHAR(50) | PK | NOT NULL |
Referenced By
- peptide_ptm_1 referencing (name)
- fixed_ptm_1 referencing (name)
- variable_ptm_1 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 (FK) | identification_id | INTEGER | ||
| spectrum_id (FK) | spectrum_id | INTEGER | ||
| description | description | VARCHAR(1024) | ||
| The description associated to this query by the search engine. | ||||
References
- identification through (identification_id)
- spectrum through (spectrum_id)
Referenced By
- peptide referencing (query_id)
query_1
(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 (FK) | identification_id | INTEGER | ||
| spectrum_id (FK) | spectrum_id | INTEGER | ||
| description | description | VARCHAR(1024) | ||
| The description associated to this query by the search engine. | ||||
References
- spectrum_1 through (spectrum_id)
- identification_1 through (identification_id)
Referenced By
- peptide_1 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 (FK) | identification_id | INTEGER | ||
| 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 (FK) | sample_name | VARCHAR(50) |
References
- identification through (identification_id)
- sample through (sample_name)
Referenced By
- run_properties referencing (run_id)
run_1
(Physical Name: run)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| run_id (PK) | run_id | INTEGER | PK | NOT NULL |
| identification_id (FK) | identification_id | INTEGER | ||
| 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 (FK) | sample_name | VARCHAR(50) |
References
- sample_1 through (sample_name)
- identification_1 through (identification_id)
Referenced By
- run_properties_1 referencing (run_id)
run_properties
(Physical Name: run_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| run_id (PK) (FK) | run_id | INTEGER | PK | NOT NULL |
References
- property_group through (property_group_id)
- run through (run_id)
run_properties_1
(Physical Name: run_properties)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| property_group_id (PK) (FK) | property_group_id | INTEGER | PK | NOT NULL |
| run_id (PK) (FK) | run_id | INTEGER | PK | NOT NULL |
References
- property_group_1 through (property_group_id)
- run_1 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 referencing (sample_name)
sample_1
(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_1 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 (FK) | database_id | INTEGER | ||
| taxonomy | taxonomy | VARCHAR(150) | ||
| 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) | ||
| searched_seq_count | searched_seq_count | INTEGER |
References
- database through (database_id)
Referenced By
- description referencing (search_settings_id)
- fixed_ptm referencing (search_settings_id)
- ion_search referencing (search_settings_id)
- msms_search referencing (search_settings_id)
- used_enzyme referencing (search_settings_id)
- variable_ptm referencing (search_settings_id)
search_settings_1
(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 (FK) | database_id | INTEGER | ||
| taxonomy | taxonomy | VARCHAR(150) | ||
| 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) | ||
| searched_seq_count | searched_seq_count | INTEGER |
References
- database_1 through (database_id)
Referenced By
- ion_search_1 referencing (search_settings_id)
- used_enzyme_1 referencing (search_settings_id)
- msms_search_1 referencing (search_settings_id)
- fixed_ptm_1 referencing (search_settings_id)
- description_1 referencing (search_settings_id)
- variable_ptm_1 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. | ||||
Referenced By
- query referencing (spectrum_id)
spectrum_1
(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. | ||||
Referenced By
- query_1 referencing (spectrum_id)
used_enzyme
(Physical Name: used_enzyme)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| enzyme_name (PK) (FK) | enzyme_name | VARCHAR(50) | PK | NOT NULL |
| search_settings_id (PK) (FK) | search_settings_id | INTEGER | PK | NOT NULL |
References
- enzyme through (enzyme_name)
- search_settings through (search_settings_id)
used_enzyme_1
(Physical Name: used_enzyme)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| enzyme_name (PK) (FK) | enzyme_name | VARCHAR(50) | PK | NOT NULL |
| search_settings_id (PK) (FK) | search_settings_id | INTEGER | PK | NOT NULL |
References
- search_settings_1 through (search_settings_id)
- enzyme_1 through (enzyme_name)
variable_ptm
(Physical Name: variable_ptm)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| ptm_name (PK) (FK) | ptm_name | VARCHAR(50) | PK | NOT NULL |
| search_settings_id (PK) (FK) | search_settings_id | INTEGER | PK | NOT NULL |
| ptm_index | ptm_index | INTEGER | ||
| ptm_type | ptm_type | VARCHAR(50) |
References
- ptm through (ptm_name)
- search_settings through (search_settings_id)
variable_ptm_1
(Physical Name: variable_ptm)
| Logical Column Name | Physical Column Name | Type | PK | Nullable |
| ptm_name (PK) (FK) | ptm_name | VARCHAR(50) | PK | NOT NULL |
| search_settings_id (PK) (FK) | search_settings_id | INTEGER | PK | NOT NULL |
| ptm_index | ptm_index | INTEGER | ||
| ptm_type | ptm_type | VARCHAR(50) |
References
- search_settings_1 through (search_settings_id)
- ptm_1 through (ptm_name)
userguide/msidbmodeld.3-desc.txt · Last modified: 2010/07/08 09:22 by 132.168.73.9
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