contamination in mass spectrometric data - (Mar/05/2014 )
Can anyone share their experience regarding contaminants that we get in MS analysis. Sometimes we get keratin and albumin in nuclear and mitochondrial fractions of cell. What are the reasons for that.
keratins can be from dust.
Even in the most pristine lab environments this can happen - and to my knowledge it has less to do with the tissue/organelle you're looking at than it does your preparation of the sample.
Our institution's MS/MS technician explained that both keratin and albumin come from handling, unfiltered air, dirty/old instruments/disposables, etc. The only way to really reduce this is to perform every step of the sample prep in a dedicated hood, away from any protein contaminants, and with dedicated/isolated tools and disposables. You should be able to see whether or not you have a contamination issue on your stained gels prior to MS (assuming you're doing protein/peptide identification in this fashion). Many high molecular weight contaminants form an intense "bar" across the top of the lanes in a 1D gel.
It's unlikely the contaminants will be completely eliminated, but they can be significantly reduced.