Hi Matt, I'm using Excel to open the mzML/mzXML files. What I am trying to do with the mzML/mzXML files is to extract just the MRM transitions and their corresponding signal intensities and use my own MATLAB program to do data analysis. I had been able to use the TPP to convert the Thermo MRM raw data to mzXML files. But so far it has not been working for the Waters MRM raw data.
Thanks, Harry On Feb 2, 11:05 am, Matthew Chambers <[email protected]> wrote: > I'm not sure what you mean by "column head[er]s". What context are you > viewing the mzML in? > > -Matt > > On 2/2/2012 12:58 PM, Harry wrote: > > > > > > > > > Hello Matt, > > > Thanks for the comments. > > I tried converting the raw data to mzML instead of mzXML as well. It > > didn't work. All I got in the mzML file is the column heads, but no > > content. > > > Harry > > > On Feb 1, 1:40 pm, Matthew Chambers<[email protected]> wrote: > >> That's not an msconvert warning. Msconvert would handle his MRM data fine > >> as mzML, not mzXML. Does > >> TPP work with mzML chromatograms yet? > > >> -Matt > > >> On 2/1/2012 3:35 PM, Joseph Slagel wrote: > > >>> Harry, > > >>> I'm not sure I can be of any more help. I'd suggest you forward your > >>> question to the ProteoWizard's > >>> mailing list ([email protected] > >>> <mailto:[email protected]><mailto:[email protected]>) > >>> and I'm sure > >>> you'll get a answer. > > >>> -Joe > > >>> On Tue, Jan 31, 2012 at 11:18 AM, > >>> Harry<[email protected]<mailto:[email protected]>> wrote: > > >>> Hello Joe, > > >>> Thank you for replying my question. > > >>> The error message I got looks like this: > > >>> ... > >>> Preprocessing function 97 > >>> !!Warning!!: ignoring function 97 with type MRM > >>> Preprocessing function 98 > >>> !!Warning!!: ignoring function 98 with type MRM > >>> Preprocessing function 99 > >>> !!Warning!!: ignoring function 99 with type MRM > >>> no scans found, exiting with error > >>> END OUTPUT > >>> RETURN CODE:65280 > >>> ###### End Command Execution ###### > >>> # All finished at Tue Jan 31 10:57:14 2012 > >>> # END COMMAND BLOCK > > >>> I also tried msconvert. The program did generate a mzXML file from > >>> the raw data, but there is no actual data (MRM transitions and their > >>> signal intensities) in the mzXML file. Would it be more useful to > >>> you > >>> to see the problem if I send you the mzXML file? > > >>> Thank you for your time. > > >>> Harry > > >>> On Jan 31, 10:40 am, Joseph Slagel<[email protected] > >>> <mailto:[email protected]>> > >>> wrote: > >>> > Harry, > > >>> > What error did you get? Did it look anything like: > > >>> > [Tue Jan 31 12:33:25 2012] EXECUTING: c:\Inetpub\tpp-bin\ReAdW > >>> -v -- > >>> > mzXML > >>> c:/Inetpub/wwwroot/ISB/data/12032011_60min_PaG_XC_HP101_01.raw > >>> > OUTPUT: > >>> > The system cannot find message text for message number 0x2331 in > >>> the > >>> > message file for Application. > > >>> > If so, then please try using msconvert instead of ReAdW. We're > >>> no longer > >>> > supporting or bundling this program with TPP. > > >>> > -Joe > > >>> > On Mon, Jan 30, 2012 at 1:45 PM, > >>> Harry<[email protected]<mailto:[email protected]>> wrote: > >>> > > Hello, > > >>> > > I was trying to use the mzXML conversion tool in PPT to > >>> convert some > >>> > > MRM raw data acquired on a Waters Xevo through direct > >>> infusion. The > >>> > > program could not do it. Has anybody had similar problem? > > >>> > > Thank you for any ideas and suggestions. > > >>> > > Harry -- 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.
