Hey Guys, I have a question regarding identification of phosphopeptide using TPP. I got a data using an LTQ-XL (using CID) and I ‘ve searched using MASCOT search engine (phosphorylation as a variable modification in S/ T/Y) . I found more than 50 phosphorylated proteins however when I use TPP to look at these phosphorylations I found none! I am wondering if all the phoshphorylation detected by MASCOT are in fact false positives. Here is what I’ve done: I use TPP v4.4 rev 1 in W7 Run MASCOT Convert *.dat to *.pepxml Run PeptideProphet (I’ve selected the icon “Use phospho information”) and ProteinProphet afterwards. Can anyone help me? Thanks in advance!
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