Proteomics data file submission to PRIDE, PXD006848

Data curation notes provided by Alex Graf via Willi Gruissem, in addition to the PRIDE deposition.

The Excel file gives the list of samples uploaded into PRIDE. here - https://fairdomhub.org/data_files/3704

The published experimental design might lead one to expect 4x3x2x7 = 168 samples.
There are more than 168 samples in the PRIDE upload for the following reasons:

First, all of the measurements from the experiment had been uploaded, including files for measurements that were repeated because of problems during the MS run. These samples are not annotated in the table.

Second, we had included 4 Gold Standard samples (2 replicates on each of the two large gels used to process all samples). These 4 gold standard samples in 7 fractions explain 28 extra samples.

Third, we did not have 168 but 166 samples in the photoperiod set. Fractions 1 and 2 of sample 43 (Photoperiod 2, bio replicate 1, tech. replicate 2) were lost during sample preparation. While the remaining fractions were measured and are included in the PRIDE upload and the table, this sample was not used in the data analysis.
Photoperiod 2 bio rep. 1 was only used with one technical replicate in the calculations.

The table “Table Sorted PP and Replicates” in the Excel file has all the relevant annotation.

由亚历克斯·格拉夫通过威廉·格鲁伊瑟姆提供的资料整理笔记，以及PRIDE数据提交的附加信息。该Excel文件提供了上传至PRIDE的样本列表，详情请见 - https://fairdomhub.org/data_files/3704。根据已发布的实验设计，人们可能会预期有4x3x2x7=168个样本。然而，在PRIDE上传中实际样本数量超过168个，原因如下：首先，实验中所有测量数据均已上传，包括因质谱运行过程中出现问题的重复测量文件。这些样本在表格中未进行标注。其次，我们包含了4个金标准样本（在每个用于处理所有样本的两个大凝胶上各进行两次重复）。这4个金标准样本在7个分馏部分中解释了额外的28个样本。第三，光周期设定中并非168个样本，而是166个样本。样本43的光周期2（生物重复1，技术重复2）的1和2分馏部分在样本制备过程中丢失。尽管剩余的分馏部分已进行测量并包含在PRIDE上传和表格中，但该样本未用于数据分析。光周期2生物重复1仅使用一个技术重复进行计算。Excel文件中的“Table Sorted PP and Replicates”表格包含了所有相关的注释。