Mass spectrometry analysis give rise to redundancies, mostly, due to multiple identifications of the same gene product present in different bands or in the same band, or different strain of T. gondii.
1-Is it wise to eliminate redundancy ?
2-What technical approach (algorithm, soft, ...) can we use to remove redundancies ?
Hi Sami,
I've found software called Scaffold to be quite useful for the purpose you're describing.
Good luck!
Hi take a look at this
http://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp
is the automation af analysis like this:
http://www.ncbi.nlm.nih.gov/pubmed/22586093
Yes, most softwares used for proteomics data analysis will now accomodate this, including Scaffold, Proteome Discoverer, ProteinPilot, Mascot and so on, provide you structure your data input accordingly (flag as "Mudpit analysis" or similar). It is absolutely necessary to eliminate redundancy from a final results list, however the software should flag this, and allow one to visualize the redundancy across different fractions/gel bands etc.
For a more specific answer you would need to put more detail to your question, i.e. how are you separating your samples, how do you obtain the MS (or hopefully MS/MS?) data, which instrument and software are you currently using etc.
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