This Excel file lists the samples uploaded in PRIDE. The table “Table Sorted PP and Replicates” in the Excel file has all the relevant annotation.
There are more than the expected 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.