Analysis of shotgun proteomics and RNA profiling data from Arabidopsis thaliana chloroplasts

The integration of data from transcriptional profiling and shotgun proteomics experiments provides additional information about the identified proteins that goes beyond their plain detection. We have analyzed results from MS/MS shotgun detection of 426 Arabidopsis chloroplast proteins and genome-wide RNA profiling to identify correlations between gene expression, protein abundance and protein characteristics that influence their detection in high-throughput proteome analyses. The integrated data analysis revealed a significant molecular mass bias for the detection of proteins that were expressed at low transcript levels. Overall, the sequence coverage of most of the identified proteins increases with transcript levels indicating a positive correlation between transcript and relative protein abundance. This does not apply to a subset of the identified proteins suggesting specific properties that alter their detection in shotgun proteomics. This integrative comparison is a suitable strategy to validate large scale proteomics data and offers an assessment of the depth of the proteome analysis and the confidence in protein identification.