mzXML reads only one run of the instrument

[matteo...@gmail.com]

Hi,

I am trying to read results of an tandem MS experiment obtained on a Synapt G2 instrument. The spectrum is obtained using ETD technique. When I run :


from pyteomics import mzxml, auxiliary

path = '/Users/matteo/Documents/MassTodon/MassTodonPy/MassTodonPy/data/'
file = path+'Ubiquitin_ETD_10 ms_1071.mzXML'

with mzxml.read(file) as reader:
for spectrum in reader:
print spectrum['intensity array']


I obtain only information on the first run. This is somehow not enough: the spectrum consists of 95 runs and apparently only the first one can be accessed with the above snippet. Is there a way to access the other 94 spectra?
I know there are 95 spectra because I can open it from R using the readMzXmlData package:


# readMzXmlFile(file)


So up till now I have to use R to do something (sic!) good and nice (double sic). Could you help me, please? I cannot stand R.

Yours,

Matteo Lacki

[Lev Levitsky]

Hi Matteo, 

Thanks for your feedback. Indeed, this happens on the latest release, but is already fixed in the development version.

You can get the code at https://bitbucket.org/levitsky/pyteomics if you don't want to wait for the new version to be released.

Best regards,

Lev

--

---
You received this message because you are subscribed to the Google Groups "Pyteomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to pyteomics+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Lev Levitsky
Institute for Energy Problems of Chemical Physics RAS
Laboratory of Physical and Chemical Methods for Structure Analysis
Leninsky pr. 38, bld. 2 119334 Moscow Russia
tel: +7 499 1378257 fax: +7 499 1378257, +7 499 1378258

[matteo...@gmail.com]

Thanks!