Matt, Thanks for the explanation. Does this mean that trapper isn't using the Agilent API? (Asking the naive trapper user question)
-Joe On Tue, Feb 16, 2010 at 1:26 PM, Matthew Chambers < [email protected]> wrote: > The delay in start up time for Agilent is a known issue. Unfortunately the > current Agilent API doesn't provide a way to get the list of scanIds in a > data file, nor a way to get a spectrum's scanId without getting its data > arrays. ProteoWizard is designed to support random access by nativeID and by > index to all of the data formats it supports, so it has to enumerate all the > spectra up front in order to get each of their scanIds. On profile data, > that takes a frustrating amount of time. > > I have a feature request pending with Agilent to get a function which > provides either a list of scanIds or a spectrum without metadata. > > Thanks for doing the comparison. I agree with Dave that the conversion time > sounds pretty long in both cases and I suspect a network share. > > -Matt > > > > bio.x2y wrote: > >> Hi, >> >> I independently used both Trapper (4.3.1) and Msconvert (pwiz 1.6.0) >> to convert a 1.4Gb Agilent MassHunter ".d" file containing ~16000 >> spectra to mzXML. >> >> Parameters: >> $msconvert --mzXML --verbose large.d >> $trapper --mzXML -v large.d large.mzXML >> >> Msconvert took 5hrs 38mins to complete, generating a 57Gb file. >> Trapper took 1hr 26mins to complete, generating a 28Gb file. >> >> I can understand the differences in size, given the differences in >> structure and precision. However, the time difference still appears >> quite high. >> >> One interesting observation is that msconvert does not start writing >> to the output file until 1hr 20min has elapsed. At that point, the >> file begins filling and the progress messages start appearing in the >> output. Trapper, on the other hand, starts filling the output file and >> reporting progress immediately. >> >> I have seen this occur now for two runs on two different days, so I >> don't think it's related to other activity on the machine. >> >> Perhaps msconvert is engaging in some preprocessing that isn't >> strictly necessary, for Agilent ".d" files at least? >> >> Thanks, >> bio.x2y >> >> >> > > -- > 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]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe Slagel Institute for Systems Biology [email protected] (206) 732-1362 -- 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.
