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Bubblebeam For SAINT (version 1.0.0)
Select a value between 0 and 1 written like 0.8.


Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things:

APOSTL calculates NSAF values for each prey based on the average spectra observed for each bait

OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome

Bubble graphs are generated for each bait where:

  • x axis is the natural log of the NSAF values
  • y axis is the observed log2 fold change (as compared to control)
  • bubble radius is proportional to the average observed spectra

OPTIONAL: bubble color corresponds to the CRAPome probability of a specific interaction in which an 80% cutoff is applied where prey with less than 80% are colored tan

APOSTL queries ConsensusPathDB for protein-protein interactions within your data and then formats the resulting network for simple cytoscape import using the "import network from file" option.


MaxQuant or Scaffold:

Select Scaffold if using Scaffold output and MaxQunat if using pepetides.txt from MaxQuant software.

List File:

SAINTexpress generated "list.txt" file

Prey File:

SAINT pre-processing generated "prey.txt" file used to run SAINTexpress

Crapome File:

Raw output from Crapome Workflow 1 query (


Specify the color of the bubbles within the graph.

If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity

Use labels:

Adds gene name labels to bubbles within the "zoomed in" graphs

SAINT Score Cutoff:

Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8)

Also used for filtering during the generation of the cytoscape network


Human, mouse, or yeast

Interaction Confidence:

Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database


  • low: 0
  • medium: 0.5
  • high: 0.7
  • very high: 0.9

List of Uniprot IDs to Include:

Text file with one column of uniprot IDs. Only the Uniprot IDs in the file will be used on the resulting bubblebeam.

List of Uniprot IDs to Exclude:

Text file with one column of uniprot IDs. The Uniprot IDs in this list will not be used in generating the bubblebeam.


Bubble Graphs:

Unfiltered Data:

Filtered by SAINT Score


SAINTexpress "list.txt" output with additional columns that were used during the analysis.