Shotgun proteomics in the study of adaptive stress responses of plant proteome

Due to oncoming climate changes, droughts, high salinity, extreme temperatures became quite common stressors universally occurring in the most of terrestrial habitats. Expansions of these changes are often accompanied with strong herbivore attacks. Due to the outstanding impact of these factors on sustainable agriculture, since several last decades, the biochemistry and molecular biology of plant stress response remains in the focus of the research interest worldwide. Thus, bottom-up proteomics became a versatile tool of plant research in general and of stress biology in particular. As plant-derived materials are recognized as an extremely complex matrix, which is rich in polysaccharides, polyphenols and hardly water-soluble proteins, their proteome is typically analyzed by gel-based techniques. However, recent advances in sample preparation techniques (first of all — protein solubilization and digestion) allowed establishment of gel-free methods for plant-derived samples. Implementation of high-throughput nano-flow reversed phase-high performance liquid chromatography coupled on-line to electrospray ionization mass spectrometry (nanoRP-HPLC-ESI-MS) gave access to data-rich datasets giving high protein identification rates. Moreover, high reproducibility of HPLC allows highly sensitive and precise quantification. Therefore, over the recent decade, shotgun proteomics became the method of choice in the study of adaptive stress responses of plant proteome. Here we address the bottom-up shotgun proteomics strategy in plant biology and discuss its application to the study of plant stress response. We also discuss the main steps of the plant proteome analysis pipeline and address emerging problems and future perspectives.