mass spectrometry proteomics psms

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4.3 years ago

mdfardin374 ▴ 10

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?

MSGFPlus proteomics mass spectrometry • 760 views

ADD COMMENT • link 4.3 years ago by mdfardin374 ▴ 10

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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 REPLY • link 4.3 years ago by h.mon 35k

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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 REPLY • link 4.3 years ago by mdfardin374 ▴ 10

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