Although responses to UV stress have been characterised at system and cellular levels, the dynamics of the nuclear proteome
triggered in this situation are still unknown, despite its essential
role in regulating gene expression and in last term plant physiology. To
fill this gap, we characterised the variations in the nuclear proteome
after 2 h and 16 h (8 h/day) of UV irradiation by using state-of-the-art mass spectrometry-based shotgun proteomics
methods combined with novel bioinformatics workflows that were employed
in the manuscript entitled “The variations in the nuclear proteome
reveal new transcription factors and mechanisms involved in UV stress
response in Pinus radiata” (Pascual et al., 2016) [1]. We employed in-gel digestion followed by a 120 min gradient prior to MS analysis. Data was processed following two approaches: a database dependent employing the SEQUEST
algorithm and custom databases, and a database independent by mass
accuracy precursor alignment (MAPA). 388 proteins were identified by
SEQUEST search and 9094 m/z were quantified by MAPA. Significant m/z were de novo sequenced using the Novor algorithm. We present here the complete datasets and the analysis workflow.