Hi,everyone, I used SILAC(lys+8, arg+10) to label my cell lines, and used TripleTOF 5600 to analyze my samples. After converting raw data to .mgf files, which were searched by Mascot, I used PeptideProphet to analyze pep.xml files. I checked the resulting interact.pep.xml files, which seemed normal. After running ASAPRatio, I found ASAPRation results show N/A for every peptide. I don't know what is wrong, because I followed TPP Demo2009. By the way, the version of TPP I used is 4.5. Thanks.
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