I'm working on the proteome (from Uniprot), as you're probably aware that there are reviewed and unreviewed proteins, however unreviewed proteins are in large quantities, but reviewed proteins are few in number and will eventually require less screening. So I was wondering if it would be acceptable to study reviewed proteins rather than unreviewed ones?
Hi Dua,
It really depends on what you are trying to decipher; if you are looking to see / identify unknown proteins in the dataset, you can certainly start with the smaller size fasta in the reviewed proteome. The unreviewed proteome, contains seqeunces which are not yet confirmed/validated using biochemical etc. tools; however, you may miss valuable hits by not using the unreviewed sequences. I suggest you start with the reviewed and move to unreviewed fastas.
Good luck!
Hediye.
Hi Dua,
There is a fantastic post with the discussion regarding your question.
https://pwilmart.github.io/blog/2020/09/19/shotgun-quantification-part2
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