My question is relative to the identification of proteins by mass spectrometry.
As you now, the last step of identification is to match identified peptides to a bank of proteins.
For human, a standard bank to use is swissprot, refseq, ... Swissprot part of uniprot is the way to identify only proteins with a high level of confidence (manually reviewed..)
But my question concern identification in Rat. There is only ~8000 rat proteins in swissprot. If we used swissprot + trembl, we will capture a lot of false positives (fragments, false splice variant , ...). Do you Know what is the gold standard for Rat? Which banks are commenly used for Rat in proteomics?
Thanks in advance.