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SAINTexpress (version 1.0.0)
the number of replicates (with largest spectral counts or intensities) to be used for probability calculation in each bait. This option is useful when some baits have more replicates than others.
SAINT can be run with the known interaction data in hand and it will incorporate the number of observed interactions into the statistics to boost identification probability.

SAINTexpress

This tool will read in a Bait File, Prey File, and Inter File and analyze them using the latest version of SAINTexpress.

1) Interactions File

Please specify an Inter file for SAINTexpress analysis. An Inter file should contain four columns: IP name, bait name, prey name, and spectral counts or intensity values, depending on the mode of quantification.

2) Prey File

Please specify a Prey file for SAINTexpress analysis. A Prey file should contain three columns: prey (protein) name, prey amino acid length, and prey gene name.

3) Bait File

Please specify a Bait file for SAINTexpress analysis. A Bait file should have three columns: IP name, bait name, and the indicator for test and negative control purifications.

4) Number of Replicates

The number of replicates (with largest spectral counts or intensities) to be used for probability calculation in each bait. This option is useful when some baits have more replicates than others.

5) Using Virtual Control Purifications by Compression

Sets the number of virtual control purifications by compression. For instance, if you wish to take 4 largest spectral counts for controls, set Number of Vitual Controls to 4 and this variable to Yes.

6) Number of Virtual Controls

Specify the number of virtual control purifications by compression.

7) Incorporate External Data Sources

To incorporate external data sources for computing the Topology-Aware Probability Score (TopoAvgP), the user must also provide the interaction database file that contains two columns: interaction identifier column and interaction/grouping information column. The first column is just for formality and thus can be filled in with anything (no white space) and it will not be utilized in the scoring. The second column must be formatted as a list of prey identifiers (consistent with the first column of the prey file) separated by a white space.

8) External Data File

Specify external data file

Please cite

  • Choi, H., Larsen, B., Lin., Z.-Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z.S., Tyers, M., Gingras, A.-C. and Nesvizhskii, A.I. (2011) SAINT: probabilistic scoring of affinity purification - mass spectrometry data. Nature Methods, 8:70-3.