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 -~----------~----~----~----~------~----~------~--~---
