1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
|
.. obo:
.. default-domain:: py
##########
OBO parser
##########
.. automodule:: pymzml.obo
******************************
Accessing specific OBO MS tags
******************************
This section describes how to access some common MS tags by their names as they
are defined in the OBO file.
First pymzML is imported and the run is defined.
>>> example_file = get_example_file.open_example('dta_example.mzML')
>>> import pymzml
>>> msrun = pymzml.run.Reader(example_file)
Now, we can fetch specific imformations from the spectrum object.
MS level:
>>> for spectrum in msrun:
... print(spectrum['ms level'])
Total Ion current:
>>> for spectrum in msrun:
... print(spectrum['total ion current'])
Furthermore we can also check for presence of parameters, therefore the
proprties of the spectrum.
Differentiation of e.g. HCD and CID fractionation:
>>> for spectrum in msrun:
... if spctrum['ms level'] == 2:
... if 'collision-induced dissociation' in spectrum.keys():
... print('Spectrum {0} is a CID spectrum'.format(spectrum['id']))
... elif 'high-energy collision-induced dissociation' in spectrum.keys():
... print('Spectrum {0} is a HCD spectrum'.format(spectrum['id']))
|
