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 Exactive

Pretty-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.json

Todo

• Get the header stream to read correctly
• Provide a metadata extractor