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.

补充文件1：表S1。通过图1b中概述的串联亲和纯化-质谱（TAP-MS）流程鉴定HIV-1与SIV的Nef互作蛋白。初始数据集需以空载体实验对照为参照进行过滤。"IPI"列提供国际蛋白质索引（International Protein Index, IPI）识别码，对应"User input"列中所列的蛋白质名称。"unique peptide"列表示用于鉴定该蛋白质的独特肽段数量，而"total peptide"列则代表匹配至该蛋白质的已鉴定肽段总数量。原始数据将以CRAPome数据库为参照进行过滤，并生成多项数值。实验出现率（ExpAP）比值指某蛋白质在对照实验中出现的次数除以已分析实验的总次数。"ExpAP calculated"列给出由"ExpAP"列计算得到的比值数值。平均谱计数（Ave SC）为该蛋白质出现的实验中肽段数量的平均值。Max SC为单次实验中检测到的肽段最高数量。通过将AveSC与ExpAP相乘，可估算得到该蛋白质在阴性对照中被鉴定的次数，以及其在被鉴定时的丰度。