Hi Ruby, You are correct: the quantitation tools need to have access to the raw (mzXML) data to extract the chromatograms from the MS1 scans. The name of the mz(X)ML files should match what is contained in the base_name attribute of the msms_run_summary tag in the pepXML file that you are analyzing -- this is typically in the same directory, though it is not necessary.
Cheers, --Luis On Wed, Feb 8, 2012 at 8:48 AM, Ruby <[email protected]> wrote: > 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. > -- 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.
