21. mzPeak metadata sample list¶
Describe the JSON format of the sample list. Multiple samples can be present in a single run in scenarios like multiplexing or pooling.
21.1 Describing individual samples¶
When the sample or samples included in the MS run are described in the data file itself, it makes tracing what a data file was for, and possibly which study it came from. This makes it possible for laboratory information management systems (LIMS) to more effectively index files and for repositories to be able to supply more detailed information when searching for a dataset. This also ensures that these details move with the raw data and do not get scattered between lab notebooks, spread sheets, or unrecorded calculations that generally do not follow the MS data beyond the person doing the data acquisition or analysis.
Common properties to record:
MS:1000001|sample numberMS:1000004|sample massMS:1000005|sample volumeMS:1000006|sample concentrationMS:1000053|sample batch- Children of
MS:1000003|sample state
The MS:1000002|sample name is structurally encoded in the JSON sample.name property.
It is also useful to record if a sample was labeled/tagged (a child of MS:1002602|sample label)
or not (MS:1002038|label free sample), and if so, what the associated channel was.
Additionally, if the Experimental Factor Ontology (EFO) is used, a wide range of properties like taxonomy, tissue type, and more are defined. This overlaps with SDRF as described below.
21.1.1 Relationship with SDRF¶
A Sample and Data Relationship Format (SDRF) (Guidelines at <https://sdrf.quantms.org)> file may be embedded in directly in an mzPeak archive as a file. This allows the entire experimental design, as defined by the data producer or in-so-far as was known at the time the data were deposited. Embedding the complete file provides the reader with broader context on the experimental design and relationship with other data files. This makes the dataset discoverable, and may maintain FAIR linkage when the file is downloaded in isolation.
When an embedded SDRF file is used, the writer SHOULD attempt to match sample names for cross-referencing. When
feasible, it should also be possible to extract sample characteristics and and factor values from the SDRF to populate
the sample.parameters.
Type: array
Items: 21.2.1 sample
21.2 Definitions¶
21.2.1 sample¶
A description (one) of the samples used to generate this dataset. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#sample.
Type: object
21.2.1.1 Properties¶
| Property | Type | Required | Description |
|---|---|---|---|
id |
string |
Yes | A unique identifier for this sample. |
name |
string |
A human-readable name for this sample that might be easier to recognize. | |
parameters |
array of param |
Yes | Additional parameters describing this sample. |
21.2.1.2 Property Details¶
id - string (required)
A unique identifier for this sample.
name - string (optional)
A human-readable name for this sample that might be easier to recognize.
parameters - array of param (required)
Additional parameters describing this sample.