MzML Ripper
This package parses MzML files and extracts data into JSON format for easier processing.
Extracts the following information:
-
MS1 Information
-
MS2 Information
-
MS3 Information
-
MS4 Information
-
For each spectrum in MS1/2/3/4:
- Masses and Intensities
- Parent of that spectrum
- Retention time of that spectrum
- List of masses
Installation
Mzmlripper is available through Pip (Python Package Index):
pip install mzmlripper --user
Source code will be made available in due course.
Dependencies
If you want to use the (optional) SPectraL hASHing functions (see https://splash.fiehnlab.ucdavis.edu/ for more details), you may want to install pySPLASH with the following commands:
git clone git://github.com/berlinguyinca/spectra-hash.git
cd spectra-hash/python
python setup.py install
Usage
Import the extractor and give it a file/directory and an output directory for the JSON files
# Import module
import mzmlripper.extractor as ripper
# Process an mzML file
ripper_data = ripper.process_mzml_file(mzml_filename, target_directory)
# Using the pySPLASH functions
import mzmlripper.splash_helpers as spl
# Add splash to each ripper function
splashed_ripper_data = spl.splash_ripper_dict(ripper_data)Output
The file output is in the following format:
{
"ms1": {
"sppectrum_1": {
"95.3423": 160,
"96.8473": 322,
"110.8476": 640253,
...
"parent": "",
"retention_time": "0.9685",
"mass_list": [
95.3423,
96.8473,
110.8476
...
]
},
"spectrum_2": {
...
},
...
},
"ms2": {
"spectrum_1": {
"101.2356": 4552,
"102.5398": 12369,
"102.9856": 845,
...
"parent": "235.6523",
"retention_time": "1.1203",
"mass_list": [
101.2356,
102.5398,
102.9856,
...
]
},
"spectrum_2": {
...
},
...
},
"ms3": {
"spectrum_1": {
"67.3434": 142,
"69.8364": 1325,
"72.9746": 3320,
...
"parent": "102.2365",
"retention_time": "1.0253",
"mass_list": [
67.3434,
69.8364,
72.9746,
...
]
},
"spectrum_2": {
...
},
...
},
"ms4": {
"spectrum_1": {
"45.2036": 1234,
"46.3210": 8853,
"49.3205": 12342,
...
"parent": "115.3256",
"retention_time": "2.0365",
"mass_list": [
45.2036,
46.3120,
49.3205,
...
]
},
"spectrum_2": {
...
},
...
}
}Authors
All software was written as part of the Cronin Lab 2019
