dear all
I've performed a shotgun experiment (DDA) on a nanoACQUITY UPLC MS system (waters) and processed raw data with PLGS software (waters). We found some proteins differentially expressed in two conditions and now a validation of these is required. I was thinking of building a library (fasta from uniprot) only with these proteins and use this as my database. Then I think to compare the retention times of the peptides found. is that correct? do you have any suggestions for me?
Thanks in advance.
best regards,
Viviana