Hi, I'm using CompassXport (Free download from Bruker, after registration), not CompassXtract
>compassxport -multi d:\data\directory\ will convert all *.yep files of the given data directory to *.mzXML files which can be read by TPP/X!Tandem. It will automatically dive into your .D directories. I used this tool successfully for converting data of the HCTultra/ETD (Bruker) and the MSD/XCTultra (Agilent). Those *.mzXML files work only for X!Tandem, not for OMSSA. For generating *.mgf files usable for OMSSA searches I use MzXML2Search, bundled with the TPP: >FOR %I IN (*.mzXML) DO MzXML2Search -mgf -ACID -M2-2 -P5 -I0.01 -B10 -T5000.0 >%I converts all *.mzXML files to OMSSA compatible *.mgf Saludos, Robert On Feb 11, 1:04 pm, Matt Chambers <[email protected]> wrote: > As Natalie suggested, Analysis.yep indicates the Bruker/Agilent YEP > format which ProteoWizard reads with CompassXtract. Msconvert will > automatically detect the format of the .d directory and use the > appropriate reader. Keep in mind the CompassXtract interface (which > supports Bruker FID/BAF and Bruker/Agilent YEP) is only licensed for > non-commercial use. > > -Matt > > Natalie Tasman wrote: > > Hello Zeyu, > > > You're using the TPP's "trapper" program. Trapper is designed for > > data from Agilent's *MassHunter* program. This data is stored in a .d > > folder. However, there is a confusing situation: two different > > Agilent formats use .d folders. Your .d folder has the different > > format: analysis.yep. I'm guessing that you're probably using data > > acquired with Agilent's *ChemStation* program. Trapper does not > > handle .yep. But, msconvert, which is included with the TPP and comes > > from the ProteoWizard (pwiz) project, might handle this type of data. > > I'm forwarding this message to the pwiz discussion list as well, and > > hopefully they can suggest a way to proceed. > > > There is an > > > -Natalie > > > On 2/10/10 11:16 PM, zeyu sun wrote: > >> Hi, I have a problem to convert the .d folder from a ETD trap to xml > >> format. I have no problem to convert .d folderto xml for spectrum from > >> Q-tof. Here is what I saw in the commend line: > > >> Settings: > >> centroid scans: 0 > > >> compress scans: 0 > >> verbose mode: 1 > >> skip checksum: 0 > >> deisotope:0 > >> requirePeptideLikeAbundanceProfile: 0 > >> relativeTolerance: 0 > >> absoluteTolerance: 0 > >> limitChargeState:0 > >> maxChargeState: 0 > > >> mzML mode: 0 > >> mzXML mode: 1 > >> input filename: c:/Inetpub/wwwroot/ISB/data/ZSMOAC.D > >> output filename: c:/Inetpub/wwwroot/ISB/data/ZSMOAC.mzXML > > >> ERROR at .\MHDACWrapper.cpp, 60: > >> HR = -2147024894 > >> OpenDataFile > > >> unable to open c:/Inetpub/wwwroot/ISB/data/ZSMOAC.D with MassHunter > >> interface > > >> *Command FAILED* > > >> by the way, the .d folder comprised of a analysis.yep file (very big, > >> which I assume is where the MS data stored), a LCDIAG.reg file, a > >> extension.baf file, a sample.mac file, 3 txt files named > >> LCMETHODAUDITTRAIL, lcparms, RUN, and a folder ETD_LONGCHIP_100128.M. > > >> Any thought how to do the conversion? > >> Thank you very much! > > >> -- > >> Zeyu Sun > > -- 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.
