Hi Matthias, [Looks like some other folks might be able to help you out directly; take the below with a grain of salt]
Most of the folks here work with LC not GC MS. However, the existing software for extracting LCMS data should at least get you started towards your own. I would start with ReAdW: http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/util/ It uses the "XRawfile" DLL. There's some minimal documentation in c:\Xcalibur\examples\xdk\ and c:\Xcalibur\Help\xdkhelp\, if you choose to install it when you install XCalibur, but I mostly end up cribbing from others, using ObjectBrowser and writing little test programs. Note that, at least for LCMS data, there are two types of data that could be stored in the RAW file: "centroid" (stick peaks, just a single mass/abundance pair for each peak), and "profile" (peaks with actual shape). You have to use the right function for each (ReAdW does this) or you get wacky data. I suspect you'll need to use a totally separate function for the EC detector. The trickiest bit I've found is the string manipulation; there are approximately fourteen million different kinds of character strings on windows, and figuring out how to convert between them all is a pain. If someone has a good reference for this, I'd love to see it. Good luck! -c brennmat wrote: > Dear all > > I am an absolute newbie and I am not sure if I came to the right > place... well, here's my question: > > I am looking for a tool that extracts chromatogram data from XCalibur > *.raw files and converts them into a format that is readable by other > software (e.g. Matlab or Octave). My *.raw files contain data from a > GC/MS system which has both an MS and an ECD (electron capture > detector; note that the data from the ECD does not contain massess, > only signal intensity as a function of time). > > I can think of two ways to achieve this: > > 1. There is already a tool available that does what I need. This might > be a converter that converts the XCalibur *.raw into a file that is > readable by Matlab or Octave. Remember that I not only need the MS > data, but also the ECD data which does not have any mass information. > Otherwise I could use XCalibur/xconvert or ReAdW, which export to ANDI > or mzXML. Is there a converter which also processes 'massless' > chromatograms? > > 2. I might try to write some code in C/C++ that does what I need. This > might be either a standalone program or a MEX or OCT binary that runs > from within Matlab or Octave. In both cases I'd need some help to get > me started on how to use the XCalibur DLL stuff in C/C++. I have never > worked with C/C++ on Microsoft Windows and I've got no clue how to > work with DLLs. Any pointers or code examples would be greatly > appreciated. > > I'd be very grateful for any hints, comments and suggestions. > > > Thanks > Matthias > > -- Christopher Mason Proteome Software (503) 244-6027 --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
