Protein from the fraction remaining after RNA extraction is useful for proteomics but care must be exercised in its application

• Protein from the fraction remaining after RNA extraction is useful for proteomics.
• Protein profiles are equivalent to those in conventional extracts.
• There are quantitative differences compared to conventional extracts.

Simultaneous isolation of mRNA and proteins from a single small biopsy specimen can be useful for integrated omics studies. Here, we have improved the method for extracting protein from the fraction remaining after RNA isolation by TRIzol reagent, for application in protein and proteome analyses. Protein yield was reduced by half, but the patterns developed on 2D gels were equivalent to conventional urea extractions. Thus, although quantitative profiles of individual proteins were different from conventionally-isolated samples, overall profiles were similar. Therefore, this particular protein source is useful for proteomics but care must be exercised in its application.