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

A total of 206 co-fractionation mass spectrometry (CF-MS) experiments were downloaded from public proteomics repositories such as PRIDE and MASSIVE, then re-analyzed with MaxQuant. This upload contains processed chromatogram matrices for all 206 experiments. Database search and protein quantitation was performed with MaxQuant (version 1.6.5.0), and potential contaminants, reverse hits, and proteins identiifed 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. Complete MaxQuant outputs for each experiment are available from the PRIDE repository under the accession PXD022048.本数据集共包含206组共分级质谱（co-fractionation mass spectrometry, CF-MS）实验数据，从PRIDE、MASSIVE等公共蛋白质组学数据库下载后，使用MaxQuant进行重新分析。本次上传内容为全部206组实验的处理后色谱矩阵文件。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，同时已过滤潜在污染物、反向命中结果及仅通过修饰肽段鉴定的蛋白质。每组实验均提供多种色谱矩阵，对应不同的蛋白质定量策略：对于无标记定量数据集，包含基于强度的绝对定量（intensity-based absolute quantification, iBAQ）、MaxLFQ、MS1强度以及谱图计数；对于细胞培养稳定同位素标记（stable isotope labeling with amino acids in cell culture, SILAC）或二甲基标记数据集，则包含同位素异构体比值。每个子目录还包含一个元数据文件，用于提供MaxQuant输出的对应色谱矩阵中每一行的详细信息。所有实验的完整MaxQuant输出文件可从PRIDE数据库获取，登录号为PXD022048。