Thermo XCalibur Method File Reader
A simple command-line program for mass spectrometry researchers that extracts and converts data from Thermo XCalibur Method (.meth) files.
Uses the olefile Python package to extract the data.
Installation
pip install XCaliburMethodReader
Usage
Help Text:
>>> XCaliburMethodReader --help
usage: XCaliburMethodReader.py [-h] [-s STREAM] [--to {text,xml,json}]
[--output OUTPUT]
FILENAME
Extracts and converts data from Thermo XCalibur Method (.meth) files.
positional arguments:
FILENAME The Thermo XCaliber .meth file to read.
optional arguments:
-h, --help show this help message and exit
-s STREAM, --stream STREAM
the data source you want to view (e.g. "Thermo
Exactive")
--to {text,xml,json} the data type to convert to.
--output OUTPUT, -o OUTPUT
File to save data into, if desired.
Print File's Directory:
>>> XCaliburMethodReader HelaStandard120.meth
Proxeon_EASY-nLC
LCQ Header
AuditData
Thermo ExactivePretty-Print Data
>>> XCaliburMethodReader HelaStandard120.meth -s "Thermo Exactive"
Method of Q Exactive HF-X
OVERALL METHOD SETTINGS
Global Settings
Use lock masses best
Lock mass injection ―
Chrom. peak width (FWHM) 15 s
Time
Method duration 120.00 min
...Extract and/or convert Data to machine-readable formats
XML:
>>> XCaliburMethodReader HelaStandard120.meth -s "Thermo Exactive" --to xml
<?xml version="1.0" encoding="utf-16" standalone="yes"?>
<InstrumentSetupMethod guid="a0742e44-9001-4c98-ac3c-7e5e366c6196" TargetInstrument="Deukalion" version="1.1" FullInternalName="Framework.Method" date="2018-11-06 10:38:12Z">
<Description>Method</Description>
<Segments>
<Segment FullInternalName="Framework.Segment" id="1">
<ScanEvent guid="553826f1-95e1-4570-a984-c77b91722f6d" id="1" FullInternalName="Deukalion.TopN.4" DescendantType="Child">
<Expanded FullInternalName="bool">false</Expanded>
...JSON:
>>> XCaliburMethodReader HelaStandard120.meth -s "Thermo Exactive" --to json
{
"InstrumentSetupMethod": {
"@guid": "a0742e44-9001-4c98-ac3c-7e5e366c6196",
"@TargetInstrument": "Deukalion",
"@version": "1.1",
"@FullInternalName": "Framework.Method",
...Save output to a file:
>>> XCaliburMethodReader HelaStandard120.meth -s "Thermo Exactive" --to json -o myfile.jsonTodo
- Get the header stream to read correctly
- Provide a metadata extractor
