This tool is a static version of the APOSTL interactive affinity proteomics analysis software that calculates the NSAF, NSAF Score, and optionally the CRAPomePCT.
The NSAF Score is the ratio of the NSAF for test preys versus control preys normalized by the number of controls. The NSAF Score performs similarly to the SaintScore in spectral counting data following a sigmoidal relationship whereas with MS1 intensity data, NSAF scoring tracks sigmoidally to the log2 fold-change. The NSAF score is designed as a less stringent alternative to the SaintScore to complement the analysis, functioning as an empirical fold-change.
CRAPomePCT is the probability of a true interaction based on the abundance of a protein in the CRAPome database.
APOSTL was developed at H. Lee Moffitt Cancer Center and Research Institute and distributed under a GNU General Public License (GPL).
1) SAINT Output File
SAINTexpress generated list.txt file.
Note: Prey IDs must be in Uniprot/Swissprot format (e.g. "EGFR_HUMAN" or "P00533").
2) Prey File
Please specify a Prey file for Bubble Graph creation. A Prey file should contain three columns: prey (protein) name, prey amino acid length, and prey gene name.
3) CRAPome File
Please specify an CRAPome file for Bubble Graph creation. An CRAPome file should contain five columns: IP name, Mapped Gene Symbol, Number of Experiments (ratio), and Average spectral counts, and Max spectral counts.
4) Interactions File
Please specify an Inter file for Bubble Graph creation. 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.