Harry, I made a modification to readmzXML for you that hopefully gets you the data in the format you want. I'll send you a link to the binary offline.
- Jimmy Harry wrote: > Hello Brian, > > I was able to generate a txt file from mzML or mzXML files using > readmzXML. Thanks! > > What I found curious was that the txt file generated from the mzML > file does not contain the precursor ion list (which is necessary for > interpreting the data), while the txt file generated from the mzXML > file does have the precursor ion list. The mzXML and mzML files being > used were converted from the same RAW data using TTP. > > I'd like to go back to my original question here again. When I used > the -b option (print brief peak list in interactive mode) with > readmzXML, it showed peak intensities for each transitions of the > specified SRM scan, on the screen. This information is what I needed, > besides those already in the txt file. Is there a way to incorporate > the SRM peak list into the txt file using readmzXML? > > Thank you for your help! > > Harry > > On Aug 6, 2:19 pm, "Brian Pratt" <[email protected]> wrote: >> Try passing it through readmzXML instead, you should be able to put the >> result of that into Excel. >> >> -----Original Message----- >> From: [email protected] >> >> [mailto:[email protected]] On Behalf Of Harry >> Sent: Thursday, August 06, 2009 1:14 PM >> To: spctools-discuss >> Subject: [spctools-discuss] Re: A question on converting RAW data of MRM >> experiments to mzXML >> >> Hello Matt, Thanks for replying to my question! >> >> I converted the my RAW date file to mzML, but had problems opening the >> mzML file in Excel. When I tried to open the file as an XML list, I >> got the message: "There is a problem with the specified XML or schema >> source". I clicked OK, then got another error message: "XML input >> Error: some data failed to import". In the end I got the spread sheet >> with column heads, but no actual data. I also tried to open the file >> as a read-only workbook, again got an error message, even though this >> time I can see part of the data appeared in the spread sheet. When I >> clicked OK on the error message, all was lost in the spread sheet. >> >> Could you enlighten me what might be the cause of this problem and how >> to open the mzML files? >> >> P.S. you mentioned that mzML format stores SRM data in a chromatogram- >> centric way, my data were collected using static infusion. I wonder >> if that would cause any problem. >> >> Thanks a lot, >> Harry >> >> On Aug 6, 8:22 am, Matthew Chambers <[email protected]> >> wrote: >>> The m/z and intensity of each transition at each scan is stored in that >>> scan's peak list in base64. So it's not human readable, but it's there. >>> Incidentally, the mzML format stores SRM data in a chromatogram-centric >>> way which is far more space and time efficient. Depending on what tool >>> you're using to analyze the data you might try the new format. >>> -Matt >>> Harry wrote: >>>> Hello group members! >>>> I encountered a problem when using the data conversion function in the >>>> TTP (v4.2 JETSTREAM rev 1, Build 200904071723) to convert my MRM >>>> experimental data in .RAW format to mzXML. >>>> In my MRM experiment setup, I had 3 transitions (i.e. 3 fragment ions) >>>> for each precursor ion. In the mzXML file that was converted from the >>>> RAW data file, for each precursor ion, it showed the "base peak >>>> intensity" and "total ion current", which is the signal intensity of >>>> the strongest transition and the sum of the signal intensity for all 3 >>>> transitions, respectively. What is also very important for my >>>> experiment, but missing in the mzXML file, is the signal intensity of >>>> the weakest transition for each precursor ion. >>>> So the question is: How can I get the individual signal intensity for >>>> all 3 transitions of a precursor ion to show up in the mzXML file that >>>> is converted from a RAW data file acquired in a MRM experiment? >>>> Thanks so much for your help! >>>> 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 -~----------~----~----~----~------~----~------~--~---
