Re-analysis of dataset PXD017646

We adopted the method used in the O-Pair article to validate the FDR calculations of O-glycopeptide search in MS-Decipher. The detailed description of the method was provided in the ‘Methods’ and ‘Evaluating O-Pair Search performance’ parts of O-Pair article (Lu et al., 2020). The results were firstly filtered for Target hits and GPSM (glycopeptide-spectrum match)-level q-value < 0.01 and score > 0. And the ‘Estimated FDRs’ were calculated by dividing the number of total GPSM by the number of GPSM, whose sequence matched with the entrapment proteins.本研究采用O-Pair研究论文中提出的方法，对MS-Decipher软件中O-糖肽搜索的假发现率（False Discovery Rate, FDR）计算结果进行验证。该方法的详细说明见于O-Pair研究论文（Lu等人，2020）的「方法」与「评估O-Pair搜索性能」章节。首先对结果进行筛选，保留靶标命中（Target hits）且糖肽-质谱匹配（glycopeptide-spectrum match, GPSM）水平q值小于0.01、得分大于0的条目。随后通过总GPSM数量与序列匹配至捕获蛋白（entrapment proteins）的GPSM数量的比值，计算得到「估计假发现率（Estimated FDRs）」。