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help/software in understanding quantitative data for 100s of peptide ids (phos)

Posted: Fri Apr 20, 2012 6:21 am
by neil777
ive spent ages develping methods to quantitate phosphopeptides and normal peptide expression.
i am comparing a cell line with or without a drug treatment. now that i have 100s of peptide quants does
anyone know of a free way to make sense of the biological meaning of the data
ideally i would like to paste a list of accession numbers and their quant values and a magical piece of software would tell me protein function, known phospo site etc. ive tried reactome which is quite good but not really for phospo sites. it seems that getting the data is only half the battle !!!!

Posted: Mon Apr 01, 2013 2:09 pm
by ChiLee
Hey Neil,

It's been a whole year since your post so you've probably sorted your issue. In case you haven't, you could try using DAVID? It's a nice webserver that lets you put in a list of accession ids (just state what they are e.g. uniprot) and it'll map and return various things e.g. GO annotations, pathways etc along with some statistics (can't recall exactly what they do). With regards to your quant, maybe you could separate them into two lists e.g. top-n highest and lowest quants and bung them into DAVID separately and see the differences?