Pros and cons of plant nuclear protein enrichment

Abstract

Nuclear proteome contains important regulatory proteins. To improve the detection of these proteins, Percoll gradient-based fractionation techniques have been developed and optimized. However, owing to the ever increasing sensitivity of identification methods based on liquid chromatography and mass spectrometry, the time and material consuming fractionation methods may no longer be necessary. Here, we show that a Percoll-based nuclear protein fractionation of tomato leaf proteome increased the number of detected proteins, but at least some nuclear proteins were lost or depleted in the process.