If you visited our office, you would quickly discover that we frequently discuss how next-gen sequencing (and specifically RNA-seq) fits in to the larger research puzzle. It’s such a powerful tool that we’re constantly learning about new applications of the technology. One of our recent conversations centered on protein mass spectrometry.
Both RNA and protein are highly dynamic, tissue specific and important regulators of cellular homeostasis. So it makes sense that RNA-seq (in this case, ribo-seq) and protein mass spectrometry are powerful approaches that are popularly used to help us gain insight into the molecular mechanisms of health and disease. But while mass spectrometry is used in a variety of contexts including identifying protein-complex constituents, post-translational modifications, and surveying protein populations in disease models, developmental time points, and your favorite organelles, RNA-seq does not allow the researcher to identify protein-complex constituents. It is certainly still a great approach for identifying transcribed products and their possible splice variants or single nucleotide variants, and this data may elucidate important regulatory events. Another advantage of RNA-seq is that it is inherently quantifiable, and at Cofactor, every project comes standard with RNA spike-ins, providing you with an important technical control allowing you to reliably compare results between samples. And as highlighted by Wang et al, 2012, RNA-seq does serve as a fantastic guide for concurrent proteomics studies or those processed in parallel.
Regardless of whether you choose mass spectrometry or RNA-seq to identify candidates, validation by established methodologies can provide you with confidence in your data.