Quantitative proteomics study on rice embryo during embryogenesis by using isobaric tags for relative and absolute quantification (iTRAQ)

Sample Info.: There are five embryogenesis stages, 6, 12, 18, 24 and 30 days after pollination (DAP). We collect the rice embryos from above five stages. Protein extraction and analysis: Embryos of the five sampling time points were used for protein extraction and One hundred micro gram extracted proteins of each sampling time point was tryptic digested and then labeled with iTRAQ 113, 115, 117, 119 and 121 for 6, 12, 18, 24 and 30 DAP resceptively. The labeled peptides were mixed together and then fractionated via SCX column to 10 fraction (named from 1 to 10). Two microgram peptides of each fraction was loaded onto a nano HPLC mounted with C 18 column and tandermed with a Q-Exactive mass spectrometer. For each fraction, three technical analysis were conducted (e.g., for fraction 5, the three injection raw files were named as 5_1, 5_2 and 5_3). Protein search: Each group of raw files (e.g., 1_1, 2_1, ... , 10_1) were combined and used for Mascot search and the search results were also uploaded in this system. F009646, F009647 and F009648 represent the mascot search result of replication 1, 2 and 3 respectively.