P: Average mass spectrum (single-dataset)
Brief description
Generate average mass spectrum based on fraction of the pixels.
Parameters
Filename (type - string)
Filename to use for the object. This can be very helpful when you want to e.g. compare or export spectra
Proportion (type - number)
Proportion of pixels to use for the task.
Normalization tag (type - string)
Tag to use for normalization.
Help
Rather than applying a normalization to the entire dataset, we apply it as needed to each task at hand.
You can compare the effect normalization has on specific task by repeating it with different normalization.
In some cases, its advised to use 'multi-dataset' normalization, in particular when doing comparisons.
Normalization name (type - string)
Name of the normalization.
More Information
This task will extract average mass spectrum for each dataset in the dataset folder.
The average spectrum will be based on the specified proportion (of pixels/frames) of the dataset.
- If the value is equal to
1.0, then all pixels will be used for this task. - If this value is less than
1.0, e.g.0.5then 50% of all pixels will be used. The 50% is selected evenly throughout the dataset.
We don't apply normalization on the entire dataset which means that we can (and should) apply normalizations on certain tasks, such as generating heatmaps. You can select normalization tag (source) and normalization name (e.g. TIC).
Dependencies (other tasks that this task might depend on)
| Depends on | Required/Optional |
|---|---|
| P: Normalization (single-dataset) | optional |
| P: Normalization (multi-dataset) | optional |
| P: Normalization (merged-project) | optional |
Dependents (tasks that might depend on this task)
| Dependants | Required/Optional |
|---|---|
| P: Mass calibration (single-dataset) | required |
| W: M/z feature detection (single-dataset) | required |
| W: M/z feature detection (multi-dataset) | required |
| W: Compare spectra (interactive, multi-dataset) | required |
| W: Compare spectra (one-vs-one; single-dataset) | required |
| W: Compare spectra (one-vs-one; multi-dataset) | required |
| W: Annotate mass spectra (single-dataset) | required |
| W: Annotate mass spectrum (multi-dataset) | required |
| W: Annotate average mass spectrum (merged-project) | required |
Attributes
| Attribute | Value | Description |
|---|---|---|
| Multiple allowed | True | Allow multiple instances of this task in a workflow. |
| Task can fail | False | Task is optional and can fail without causing the entire workflow to fail. |
| Step can fail | False | Sub-tasks of this task can fail without causing the entire task (and workflow) to fail. |
| Requires ion mobility | False | Task requires ion mobility data. |
| Task can fail (with ion mobility) | False | This task uses ion mobility data but it is allowed to fail, without causing the entire workflow to fail. |
| Allowed in reference dataset | True | Task is to be performed on a 'reference' dataset. This will allow for multiple analyses to be performed on the same dataset, without cluttering or duplicating certain tasks (unused at the moment). |