Comprehensive proteomics data on whole rice grain of selected pigmented and non-pigmented rice varieties using SWATH-MS approach

The proteome data of whole rice grain is considerably lim-ited particularly for rice with pigmentations such as black and red rice. Hence, we performed proteome analysis of two black rice varieties (BALI and Pulut Hitam 9), two red rice varieties (MRM16 and MRQ100) and two white rice varieties (MR297 and MRQ76) using label-free liquid chromatography Triple TOF 6600 tandem mass spectrometry (LC-MS/MS). Our aim was to profile and identify proteins related to nutri-tional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits based on peptide-centric scor-ing from the Sequential Window Acquisition of All Theoret-ical Mass Spectra (SWATH-MS) approach. Both information dependent acquisition (IDA) and SWATH-MS run were per-formed in this analysis. Raw data was then processed us-ing ProteinPilot software to identify and compare proteins from the six different varieties. In future, this proteomics data will be integrated with previously obtained genomics [1] and transcriptomics [2] data focusing on the above nu-tritional and quality traits, with an ultimate aim to develop a panel of functional biomarkers related to those traits for future rice breeding programme. The raw MS data of the pigmented and non-pigmented rice varieties have been deposited to ProteomeXchange database with accession number PXD018338. (c) 2020 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license. (http://creativecommons.org/licenses/by/4.0/ )