Parameter options
There are several options available for processing and visualizing the data.
1. Primary filter:
All preys that satisfy this score filter for at least one bait will be displayed in the dot plot. If a
prey satisfies this filter for at least one bait, all the quantitative values for this prey –
even those that did not satisfy the cutoff in particular bait-prey pairs - will be returned. Prey
confidence be indicated by the circle edge as shown below:
2. Secondary filter:
Interactions that do no pass the primary score filter but pass this secondary filter will be marked with an
intermediate intensity in the dot plot. Interactions that do not pass either filter will be marked with
a low intensity edge. The secondary filter can be adjusted depending on the dataset to allow a greater
or lesser number of interactions into this “medium” confidence range.
3. Minimum abundance value:
In addition to the above filter requirement, a prey must have an abundance value (e.g. spectral count) above
this minimum to be included in the analysis. As with the primary filter cutoff, once a prey passes
this threshold for one bait, all the values for this prey are returned for all baits, whether or not
they pass the threshold for this specific pair.
4. Maximum abundance value:
Any preys with an abundance value (e.g. spectral count) above this cutoff will be capped at this maximum in the output
images. This is to give greater visual dynamic range for lower values when outlier
preys with very high abundance are present. This cutoff will be dependent on the instrument
and interaction method used and should be selected based on the data set.
5. Control subtraction:
The average value of a prey across control samples will be subtracted from the detected value for the bait
if this is set to "yes". The quantitative value for the prey becomes the value above and beyond what is seen
across the control samples. Specify the column to use for controls in the adjacent "Control column" field.
6. Normalization (none by default):
No normalization is applied by default, but when baits in the same dataset have been run on
instruments with varying sensitivity or dynamic range, normalization should be applied. The
options for normalization are to divide by the total abundance for all proteins identified
in the run or normalize based on a specific prey.
Normalization will be applied after control subtraction if both are specified.
7. Log transform (default no):
If desired, data can be log-transformed by base 2, base 10 or natural. Log transformation will be performed
after control subtraction and/or normalization if these are also specified.
8. Color scale (default blue-black):
Various options are available for the fill and edge color, and can be applied independently to each.
