I am currently working on proteome analysis of a cell line. I have done LC-MS/MS of the trypsin digested sample and I want to identify the proteins in it. How can I analyze my data using Agilent Bioconfirm B.07.00 ? The quick start guide of the software suggests that sequences from a fasta formatted database can be pasted in the sequence editor window. I tried it with 5-10 protein sequences from the fasta file of the cell proteome (downloaded from uniport) but that doesn't seem to be useful because it matches these protein sequences with the compound list but reports as if they are part of a single protein. What is the right way to identify proteins using Bioconfirm? Can I use Bioconfirm for online database search -such as uniport, swissprot for single or multiple taxonomies?