Python script dta2ms2.py in src/python produces ms2 files where the mass on the Z line is one proton too low (i.e. is for precursor neutral mass, rather than M+H). The mass on the S line should be checked for correctness also when the Z line mass is fixed.
Could you try this patch?
Thanks,
Sean
Hi Sean,
I didn't receive any attachment. ???
Jeff
On Mon, 13 Jan 2014, sjoemac wrote:
To get it you have to go to the sourceforge issue tracker. It's attached
there.
Bill
On Mon, Jan 13, 2014 at 1:40 PM, Jeff Howbert howbert@users.sf.net wrote:
Related
Issues:
#98The Z line mass in the ms2 file doesn't quite agree with the M+H mass in dta (off in the 3rd or 4th decimal place). This is because the script first subtracts mass_h, then adds back mass_p. Wouldn't it be preferable to use mass_p throughout, and get rid of mass_h? This would be arguably closer to physical reality.
I checked a couple of S line masses, and they look right.
Ok, how about this one?
That works perfectly on the particular set of 10 dta files I wanted to convert. I didn't test it on anything else.
I can't say how it would do if there were multiple dta files with different charge states per scan. As I read the code, it looks like it would only handle up to 2 dta files/charge states per scan. Is this correct?
How does it work from here? Will you (Sean) commit the patched version?
Yes, it can handle only up to two charges per scan. Since we only observed that with the dta files that we were given, that is what we stuck with. We can extend it to handle multiple charges but I think that there may be a converter in proteowizard that we should check out. If you okay the current version, I'll take that as a code review pass and commit the new version. Then I'll work on the next dependent issue.
OK, consider it officially code-reviewed and approved. Thanks for fixing it.
Fixed as of rev. 16288