I need to extract

[amnahsiddiqa]

I need toe extract a cvparam ; MS:1000130 for polarity of scans ; looking at #219 ; I wanted to know can we not access any information using accession like "MS:1000130" directly; it might be a naive question but I am just getting started; '

Many Thanks, Amnah

[MKoesters]

Hi Amnah,

Accessing the polarity can be done using the tag you posted.

In [1]: import pymzml                                                                         

In [2]: with pymzml.run.Reader('/home/manuel/Data/Proteomics/mzML_examples/200414_HILIC_pos_Ph
   ...: ospholipid_Soy-Soybean Phospholipid.mzML') as run: 
   ...:     for spec in run: 
   ...:         print(spec["MS:1000130"]) # positive scan 
   ...:         print(spec["MS:1000129"]) # negative scan 
   ...:         break 
   ...:                                                                                       
True
None

In [3]:  

You could do the same thing using the names instead of the MS tags

In [2]: with pymzml.run.Reader('/home/manuel/Data/Proteomics/mzML_examples/200414_HILIC_pos_Ph
   ...: ospholipid_Soy-Soybean Phospholipid.mzML') as run: 
   ...:     for spec in run: 
   ...:         print(spec["positive scan"]) # positive scan 
   ...:         print(spec["negative scan"]) # negative scan 
   ...:         break 
   ...:                                                                                       
True
None

Currently, its a bit awkward, as you see the return value of spec["MS:1000130"] is True, since its actually a positive scan. A return value of None would mean, that the tag (in this case MS:1000129) was not found.

Loading a run measured in negative mode would result in spec["MS:1000130"] returning None and spec["MS:1000130"] returning True

EDIT:

In [3]: 'negative scan' in spec                                                               
Out[3]: False

In [4]: 'positive scan' in spec                                                               
Out[4]: True

In [5]: 'MS:1000129' in spec                                                                  
Out[5]: False

In [6]: 'MS:1000130' in spec                                                                  
Out[6]: True

would also work and is probably the best method :)

Hope this help and feel free to ask if you need more information :)

Best, Manuel

[amnahsiddiqa]

hey Manuel, Thanks much. Closing the issue now.