Hi RG community,
I run LC-MS/MS experiments on a Thermo VelosPro Orbitrap, and I often need to share the raw data (chromatograms and spectra) with colleagues. Sometimes, devil is in the detail, so screencapturing is not the route to go! Does anyone know any software that will open .raw or mzML (or any other form that could be exported from .raw) files so others can open and browse the data? I.ve tried SeeMS from Proteowizard, but I dont find it very user friendly, specially for browsing LC-MSMS data that has MS and MSMS spectra.
Thanks!!!
Alex
Unfortunately all manufacturers of proprietary LC and MS software take good care precisely against such situations. Exporting raw data so that everyone can see them without having the software is anathema to them. I'm afraid everyone who needs to browse such data must have the appropriate software installed.
Thanks Julius and Markus,
Just as a follow-up, I've tried SeeMS from ProteoWizard which allow you to directly open .raw files but navigating through the LC signals and the related MS and MSMS is a little clumsy (you can't just click on a timepoint on the chromatogram and view the related MS and MSMS signal). I found a similar situation with Batmass, although their user interface is much better than SeeMS's.
Regarding the proprietary software, I hope some day vendors realize that making their data easily exchangeable is a GREAT competitive feature and could be decisive when choosing which instrument to buy! Bill Gates saw this with its free distribution of MS-DOS, and thanks to that, dominated the OS market with Windows for decades!
I'll give mzmine a try, thanks for your feedback!
Alex
Markus,
It's nice (or not!) to hear we've had similar problems... I always wonder if this fault could have been due to some incompatibility with my computer system or OS...
MZMine2 is more flexible and versatile than SeeMS. I has extended functionality, and WILL allow you to click within a chromatogram to view the associated MS (and MSMS) spectra. Once you are in the MS window, you can 'slide' to the next spectra sideways with the arrow keys (previous or next scan), however, there is no 'Marker' or indicator on the chromatogram window to see exactly the Rt of the scan you are viewing! You have to guess by looking at the MS header. This is a little annoying, specially when browsing DDA LC-MSMS experiments.
I'll keep looking but MZMine2 is the best option so far.
Cheers
Alex
Any chance you can just export the spectrum list of m/z and z into a text file?
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Proteins