Thanks! I will try to figure out if I have a naming problem, as I tried putting mzXML file into same folder, now will look in detail according to your instruction. Thanks! R
On Thu, Feb 9, 2012 at 1:24 PM, Luis Mendoza < [email protected]> wrote: > 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. > > -- 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.
