20210406 Whitney Heavner, Ph.D. Stephen EP Smith, Ph.D. Seattle Children's Research Institute ===== This dataset contains the raw XML and PBX (bioplex protocol) files necessary for performing adaptive non-parametric analysis with an emprical alpha cutoff (ANC) to identify high-confidence IP_Probe pairs, here called "PiSCES" for proteins in shared complexes detected by surface epitopes, that are signifianctly differently associated between two conditions. ==== The XML files serve as input for ANC. The PBX files, which are readable by the Bio-Plex Manager Software, contain information pertaining to the layout of each 96-well plate used in the study, including the order of the samples, the IP bead regions, and the order of the probes on each plate. This information is necessary metadata for performing ANC.  ==== For experiments with 2 plates (_P1 and _P2), the order of the probes on plate P1 are Fyn, PSD95, NMDAR1, NMDAR2A, NMDAR2B, mGluR5, Shank3, Homer1, Homer1a, and PI3K; the order of the probes on plate P2 are GluA1, GluA2, Syngap, Sap97, NL3, Ube3a, CaMKIIa, SAPAP, panShank, Shank1, and PIKE. The exception is the set of HomeostaticScaling_48hr_ samples #5-8, which have an additional probe, Fyb, at the end of plate P1. ==== For experiments with 3 plates (_P1, _P2, and _P3), the order of the probes on plate P1 are Fyn, PSD95, NMDAR1, NMDAR2A, NMDAR2B, mGluR5, Shank3; the order of the probes on plate P2 are Homer1, Homer1a, and PI3K, GluA1, GluA2, Syngap, Sap97; the order of the probes on plate P3 are NL3, Ube3a, CaMKIIa, SAPAP, panShank, Shank1, and PIKE.