(A) Interactions between core components of the CIA machinery (i.e., Tah18, Dre2, Cfd1, Nbp35, Nar1, Cia1, Cia2 and Mms19) identified by TAP-MS (tandem affinity purification (TAP) coupled to protein identification by mass spectrometry) with additional STRING evidence. Baits used for affinity purifications are represented as either red (CIA2) or olive diamonds, and preys are shown as grey diamonds. The interaction network around the core CIA components is extended by nodes imported from the STRING database with reported connections to baits and preys identified in our screen with a STRING confidence score >0.9. Edges between all nodes and their attributes correspond to bait-prey interactions of different confidence levels, either by probabilistic scoring (SAINT) of TAP-MS data and/or from experimental data (STRING). Thick green lines depict high confidence interactions observed by TAP-MS, which, in addition, are supported by experimental evidence in STRING. Thick black lines indicate robust connections, resistant to changes in parameters specified in the SAINT algorithm (SAINT score >0.8, and robustness >0.5). Thin grey lines represent connections of lower confidence level, which are sensitive to changes in parameters for the SAINT algorithm (>0.8 SAINT, robustness of <0.5). Dashed green lines show interactions observed with a SAINT score threshold between 0.7 and 0.8, and with additional experimental evidence. Dashed grey lines are interactions only reported in STRING with a STRING confidence score >0.9. We summarized nodes in a semi-automatic manner, and performed a GO enrichment analysis on the resulting clusters. Clusters were defined by STRING nodes that only had one neighbor which had to be either a prey or bait from our screen. Three additional clusters were defined manually based on common neighborhood. (B) Detection of selected CIA protein interaction partners by identification of unique peptide numbers. TAP was performed with CIA-TAP fusion proteins as baits and associated partners identified via mass spectrometry. The amount of unique peptides referring to selected interaction partners of each CIA protein was determined (n = 4). As a control, we used the strain SC0000, which does not express any TAP-fusion protein. (C) Interactions between the CIA proteins and some prominent potential partners were verified by dedicated co-IP experiments (Co-IP). Verification procedures are represented by different colors. Green: Detection via TAP-MS (based on identification of unique peptides, see also part B). Blue: Co-IP using C-terminally HA-tagged proteins as baits in WT background. Yellow: Co-IP using HA-tagged proteins as baits in a strain depleted for the early-acting CIA component Nbp35. Orange: Interactions reported by a previous systematic analysis (Krogan et al., 2006).