Coverage
How many proteins can you detect in a typical proteomics analysis?
14/05/15 09:39
This is like the answer to 'how long is a piece of string?'. The four factors that dictate the length of the identification list in a typical proteomics experiment are:
Complexity: the number of proteins in the sample Dynamic range: the range of concentrations of those proteins Available material LC-MS Instrument being used
That being said, for a modest run, appropriately replicated, we’d expect to recover data for between 1500 and 2000 proteins with good confidence in a label-free analysis of mammalian cells. If the sample is plasma/serum or cell culture medium that contains serum, then the marked bias in specific proteins will impair the ability to reach to the depths of the proteome, and pre- fractionation is usually the way forward. We do not usually get involved in these pre fractionation steps.
Complexity: the number of proteins in the sample Dynamic range: the range of concentrations of those proteins Available material LC-MS Instrument being used
That being said, for a modest run, appropriately replicated, we’d expect to recover data for between 1500 and 2000 proteins with good confidence in a label-free analysis of mammalian cells. If the sample is plasma/serum or cell culture medium that contains serum, then the marked bias in specific proteins will impair the ability to reach to the depths of the proteome, and pre- fractionation is usually the way forward. We do not usually get involved in these pre fractionation steps.