Hi Brendan, Skyline sounds like a pretty nifty tool. I'll try it and let you know what I think.
Thanks much! Harry On Aug 7, 4:33 am, Brendan <[email protected]> wrote: > Hi Harry, > I'd like to introduce the software I have been working on for the past > year, Skyline, for both building MRM methods and analyzing the > results. It is freely available at: > > http://proteome.gs.washington.edu/software/skyline > > And I am working on making it open source as part of the ProteoWizard > project. It imports several formats directly, without needing > conversion, and its customizable reports (through File / Export / > Report) allow you to export rich tabular data to CSV for further > analysis in Excel or other statistical package, such as R. > > I have created several instructional videos on the site to give you a > feel of what is possible, and how to achieve what you want. > > The site also has a support board, if you decide to use it and need > further help. > > Good luck with your MRM analysis. > > --Brendan > > On Aug 6, 8:54 pm, Jimmy Eng <[email protected]> wrote: > > > 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 -~----------~----~----~----~------~----~------~--~---
