As we know, the mass spectrometry data can only reflect the fraction of the sample that gets injected.
Even the best mass spectrometer in the world can only detect the portion of the proteome that is successfully extracted and conserved across the sample prep workflow—so it is critical that the extraction buffer and denaturants that are employed are optimal to recover the entire biological proteome.
Sodium dodecyl sulphate (SDS) also known as sodium lauryl sulfate, is recognized as one of the best detergents for solubilizing protein.
Every proteomicist has their own list of reasons for avoiding solvent-based precipitation. If only we could eliminate these drawbacks.
You’ve just spent weeks nurturing or gathering your precious protein samples. By your calculations, there should be just enough material to complete your experiments. The workflow begins; an extraction, a purification step, maybe even some trypsin, then off to the mass spectrometry lab. But when the results finally come back, the data are, shall we say, beneath your expectations. But why?
Knowing that precipitation can easily be used for reliable recovery, I also wanted to make it simple. I envisioned a device where protein solution, containing all their impurities, combined with organic solvent, and with the push of a button, purified protein is separated from the solvent. I assumed we could buy some type of device to do just that but quickly realized no such tool had yet been made. So I made one.