ProteinCenter alternative? - (Mar/11/2013 )
maybe something at expasy?
Just to clarify my work flow a little -
<*>Digested a whole cell lysate
<*>Paragon search of collected masses from each of the MuDPit fractions in ProteinPilot
This yielded a long list of protein IDs. It would be possible to go down the list of IDs and look them up individually using UniprotKb (or something like that on expasy), but this process would be quite time consuming. I know that ProteinCenter can do this for a data set at once, but we don't currently have a license for that software.
I asked this question on another forum, one of the posters showed me a solution that works perfectly for what I need.
STRAP - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2787672/