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Hello,
Many thanks for developing mMass. I would like to compare experimental spectrum to theoretical one, trying to match different peptides modifications. I would like to add different isotopic spectra generated by mMass to make a unique spectrum and also to subtract spectra from a spectrum. Is there such features in the GUI? Are such functions implemented in the code?
Regards.
Hello
unfortunatelly, these features are not available yet. Maybe in some future release.
Thanks for your answer.
How long would it take to implement such features? I am quite good at C programming and have already a small experience in Python.
Would it be possible that you set up the graphical part, and that I implement the rest? I think it would take a long time to learn the graphical interface.
Don't hesitate to contact me off-line.
Regards.
Hello,
I did couple of experiments with python and basically, it works - I can do simple operations such as A+B and A-B with two scans.
Unfortunately, there are some problems. Typically, every mass spectrum has a different x-raster so I have to "zip" those A,B together to be able to do mathematical operations. It is time consuming and significantly increase the number of data points. Maybe some function to "simplify" resulted data?
Dear Martin,
Sorry for late answer, I did not check the forum oftenly; an automatic mail when an answer is posted would be nice, but I didn't find the option.
My objective is mainly the analysis of one experimental spectra, ie versus theoretical spectra obtained from mMASS. So I guess there is no problem on x sampling. I think the main challenge is programming on the graphical interface.
Regards.
Hello,
subscribing feature has been activated for the forum.
If you are interested, I can give you my current development state of mMass 3.9 for testing. Just send me an email to support(at)mmass.org and platform you are using and I'll send you some download link. It would be nice to have your comments before posting official release.
The issue of the x-axis sampling is going to be a pervasive one: I've found that it's quite rare to get perfectly identical sampling, and manufacturers like Bruker will only acknowledge that the way they deal with it in software involves binning and is "non-trivial".
I've written some software that deals with it via spline interpolation, but it's difficult to avoid artifacts unless you're very careful.
Hi Jonathan,
you are right. This feature is not easy to implement. I hope I will soon be able to code it in C to be faster at least. But still, you will end up with extreme amount of data. I have never found any usage for this feature in my data processing but it was requested couple of times by other users :-) If you find any good algorithm for this, please let me know.
Martin
Finally I've started to learn programming in C. At least the math functions in spectrum processing panel will be much fastter in the next version.
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