Systematic reanalysis of co-fractionation mass spectrometry data: processed chromatograms

This upload contains processed chromatogram matrices for 206 CF-MS experiments. Database search and protein quantitation was performed with MaxQuant (version 1.6.5.0), and potential contaminants, reverse hits, and proteins identified only by modified peptides were filtered out. Multiple chromatograms are provided for each experiment, corresponding to different protein quantitation strategies. These include iBAQ, MaxLFQ, MS1 intensity, and spectral counts, for label-free datasets, and the isotopologue ratio for SILAC or dimethyl labelling datasets. Each directory also contains a metadata file, which contains further information about each row in the corresponding chromatogram matrices output by MaxQuant. In addition to processed chromatograms, which are provided in the "Chromatograms" directory, the upload also contains the raw output files (proteinGroups.txt) from each MaxQuant search. These files are provided within the "Protein groups" directory. Complete MaxQuant outputs for each experiment are available from the PRIDE repository under the accession PXD022048.本上传数据集包含206个色谱-质谱（CF-MS）实验的已处理色谱矩阵。本次分析的数据库搜索与蛋白质定量工作均通过MaxQuant（版本1.6.5.0）完成，并对潜在污染物、反向命中蛋白以及仅通过修饰肽段鉴定得到的蛋白进行了过滤剔除。每个实验均附带多组色谱矩阵，对应不同的蛋白质定量策略：无标记数据集可选用iBAQ、MaxLFQ、MS1强度以及谱图计数四种策略，而SILAC或二甲基标记数据集则可选用同位素异构体比值策略。每个子目录还包含一个元数据文件，其中详细记载了MaxQuant输出的对应色谱矩阵中每一行的补充信息。除了存放在"Chromatograms"目录下的已处理色谱矩阵外，本上传数据集还包含每次MaxQuant搜索得到的原始输出文件（proteinGroups.txt），这些文件存放于"Protein groups"目录中。所有实验的完整MaxQuant输出结果可从PRIDE数据库以登录号PXD022048获取。