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W: Process PASEF-MS2 imaging data (single-dataset)

Brief description

Parse PASEF imaging data and export data.

Parameters

MS2 tag (type - string)

Tag (glob pattern) to recognize the MS2 dataset(s) by.

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.

MS/MS library (type - array)

Library to find tentative matches.

Help

PASEF library is either MSP or Parquet file. At the moment, we don't support user-provided libraries.

If you would like to use your own library, please get in touch with Lukasz to discuss further.

Sum no. frames (type - integer)

When generating 'heatmap' spectra, sum this many frames to generate mass spectrum.

Peak picker (type - string)

Peak picker to use.

Auto SNR thresholding (type - boolean)

Automatically determine signal-to-noise ratio for each target.

SNR (type - number)

Signal-to-noise ratio.

Min. intensity (type - number)

Minimum intensity.

Plot style (type - array)

Style of the generated figures.

Colormap (type - string)

Colormap to use for the image.

DPI (type - integer)

DPI of the image.

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

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 True 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).