17. mzPeak metadata file description¶
Describe the JSON format of the file description section
17.1 Use cases¶
17.1.1 Listing summary information about the type of measures in the file¶
The [file_description.contents] array can hold parameters that are children of MS:1000524|data file content. This includes spectrum types (e.g. 1000579|MS1 spectrum, 1000580|MSn spectrum, MS:1000805|emission spectrum, etc.), chromatogram types, polarity, and modifiers like children of MS:1000525|spectrum representation.
This may also cover acquisition methods MS:1003213|mass spectrometry acquisition method which writers can use to signal strategies for downstream tools. This information is specialized and writers will need to take care when producing new files that the expected invariants are not broken.
17.1.2 Enumerating source files for provenance tracking¶
The file_description.source_files array of 17.4.1 source_file lists all of the component files that were used to build this file. For many run formats, that would be a single file, or it might be many files for instruments that write directories like MS:1001509|Agilent MassHunter format or that use an anchor file like MS:1000562|ABI WIFF format. Each file's checksum is recorded so that it is possible to verify that all input files are the same for equivalent reconstruction.
When converting derived files, they SHOULD be included in the list as additional source files.
Type: object
17.2 Properties¶
| Property | Type | Required | Description |
|---|---|---|---|
contents |
array of param |
Yes | Parameters describing the contents of the file, such as types of spectra. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#fileContent |
source_files |
array of 17.4.1 source_file |
Yes | List of all files used as data sources for this mzPeak file. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#sourceFileList |
contacts |
array of 17.4.2 contact |
Persons or entities responsible for the data contained here. |
17.3 Property Details¶
contents - array of param (required)
Parameters describing the contents of the file, such as types of spectra. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#fileContent
source_files - array of 17.4.1 source_file (required)
List of all files used as data sources for this mzPeak file. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#sourceFileList
contacts - array of 17.4.2 contact (optional)
Persons or entities responsible for the data contained here.
17.4 Definitions¶
17.4.1 source_file¶
A data file that was read in order to produce this mzPeak file. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#sourceFile
Type: object
17.4.1.1 Properties¶
| Property | Type | Required | Description |
|---|---|---|---|
id |
string |
Yes | A unique identifier for this source file. |
name |
string |
Yes | The name of the source file, not including parent directory |
location |
string |
Yes | The path to the source file, URI encoded. This may include file:// protocols and UNC paths |
parameters |
array of param |
Yes | Additional parameters describing this source file, like checksums, nativeID format, or file format |
17.4.1.2 Property Details¶
id - string (required)
A unique identifier for this source file.
name - string (required)
The name of the source file, not including parent directory
location - string (required)
The path to the source file, URI encoded. This may include file:// protocols and UNC paths
parameters - array of param (required)
Additional parameters describing this source file, like checksums, nativeID format, or file format
17.4.2 contact¶
A person or entity that is responsible for some portion of the data or processing that resulted in this archive. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#contact
Type: object
17.4.2.1 Properties¶
| Property | Type | Required | Description |
|---|---|---|---|
contact_name |
string |
The name of the contact person. This is equivalent to MS:1000586|contact name (http://purl.obolibrary.org/obo/MS_1000586) |
|
contact_affiliation |
string |
The home institute of the contact person. This is equivalent to MS:1000590|contact affiliation (http://purl.obolibrary.org/obo/MS_1000590) |
|
parameters |
array of param |
Yes | Parameters describing the contact, such as name, organization, email, website, or address. |
17.4.2.2 Property Details¶
contact_name - string (optional)
The name of the contact person. This is equivalent to MS:1000586|contact name (http://purl.obolibrary.org/obo/MS_1000586)
contact_affiliation - string (optional)
The home institute of the contact person. This is equivalent to MS:1000590|contact affiliation (http://purl.obolibrary.org/obo/MS_1000590)
parameters - array of param (required)
Parameters describing the contact, such as name, organization, email, website, or address.