I'm running the TPP via Petunia. Our Sequest cluster cannot currently be accessed via the TPP, so I currently convert .RAW to mzXML via MSConvert, then search on the cluster. I take the Sequest search results and copy them into TPP data folder and process them. This has worked well for me for non-quant data. However, I have tried doing this now with SILAC data, where I see peptides of both heavy and light versions, and ASAPratio tells me ". . . importing ASAPRatio protein ratios . . . and pvalues . . . Not enough data for Gaussian fitting. no pvalues available for this dataset"
I'm wondering if ASAPratio requires more than just the Sequest search results, but also the mzMXL file or something else - as I'm guessing it can't get chromatographic info from sequest output? If it needs to have another file type also, will it work if I place it in the same folder in the TPP data directory as I place the search results? Thanks! Ruby -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
