MOESM1 of The autophagy protein ATG9A promotes HIV-1 infectivity

Additional file 1: Table S1. Identification of HIV-1 and SIV Nef interactors by the TAP-MS protocol outlined in Fig. 1b. Initial datasets were filtered against the experimental control of the empty vector. The “IPI” column provides the International Protein Index identification code referring to the name of the protein in the “User input” column. The “unique peptide” column indicates the number of distinct peptides used to identify the protein whereas the “total peptide” column indicates the total number of identified peptides matched for the protein. Raw data were filtered against the CRAPome database and several values were generated. The experiment appeared (ExpAP) ratio indicates the number of times that protein appeared in a control experiment divided by the total number of experiments analyzed. The column “ExpAP calculated” provides the value of the calculated ratio from the “ExpAP” column. The average spectral count (Ave SC) is the average number of peptides in the experiments where the protein appeared. Max SC is the highest number of peptides found in a single experiment. By multiplying AveSC and ExpAP, we obtained an estimate of both the number of times the protein was identified in a negative control and its abundance when it was identified.