Question: mass spectrometry proteomics psms
0
gravatar for mdfardin374
5 months ago by
mdfardin37410
mdfardin37410 wrote:

Hi, I have translated a genome sequence into six frame and it produced 10 million ORF with a database size of 120 MB. Can I run MSGFplus(20190703) in one go or should I split it into two or three parts? Is MSGFplus database size independent?

ADD COMMENTlink modified 5 months ago • written 5 months ago by mdfardin37410

Did you translate the whole genome into ORFs? Are you sure this is what you need? This certainly is not a high quality database to use for any purpose.

Probably what you want is to predict the proteins from the genome, or even better, find a good annotation for the genome - is the genome publicly available? Is it already annotated?

ADD REPLYlink written 5 months ago by h.mon32k

Yes I did translate whole genome into six frame and the aim is to find unannotated proteins. The genome is publicly available and it is not well annotated. There are many reports of such kinds of work, however, I am confused about the size of database

ADD REPLYlink written 5 months ago by mdfardin37410
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