Linux command line execution

linux-command-line-execution

Summary

Execute MSConvert on a Linux system (Ubuntu 20.04 or compatible) to convert vendor-specific raw mass spectrometry data (ThermoFisher .raw, Agilent .d) into MSThunder-compatible formats. This skill bridges raw instrument output and downstream deep-learning-based pollutant identification.

When to use

You have vendor-specific raw mass spectrometry data (ThermoFisher .raw, Agilent .d, or equivalent) that must be converted to a format compatible with MSThunder analysis for nontargeted identification of unknown organic pollutants in water, and you have access to a Linux environment (Ubuntu 20.04 or compatible).

When NOT to use

• Raw data is already in mzML, mzXML, or another format already compatible with MSThunder — skip conversion and proceed directly to analysis.
• You do not have access to a Linux environment or cannot install MSConvert; alternative preprocessing workflows or vendor-supplied converters may be required.
• Input data is from an unsupported vendor or instrument type for which MSConvert does not provide conversion support.

Inputs

• Raw mass spectrometry data file (ThermoFisher .raw, Agilent .d, or vendor-equivalent format)
• Linux environment with MSConvert installed (Ubuntu 20.04 or compatible)
• Target output format specification (mzML or equivalent MSThunder-compatible format)

Outputs

• Converted mass spectrometry data file in MSThunder-compatible format (mzML or equivalent)
• Converted file ready for batch processing or interactive analysis in MSThunder

How to apply

Install and configure MSConvert on Ubuntu 20.04 or a compatible Linux system. Obtain the vendor-specific raw data file(s) (ThermoFisher .raw, Agilent .d, or equivalent format) and place them in an accessible directory. Execute the MSConvert command-line tool, targeting an output format compatible with MSThunder (typically mzML or mzXML). Validate the converted file for integrity and format compliance (e.g., presence of MS1/MS2 spectra, correct precursor/retention time metadata). Return the converted file to the host system for subsequent analysis using MSThunder's interface or batch-processing pipeline.

Related tools

• MSConvert (Command-line tool that performs the conversion of vendor-specific raw mass spectrometry data into MSThunder-compatible output formats)
• MSThunder (Deep learning-based nontargeted analytical framework that receives the converted data for identification of unknown organic pollutants) — https://github.com/LQZ0123/MSThunder
• Ubuntu 20.04 (Operating system environment in which MSConvert and the raw data conversion workflow are executed)

Evaluation signals

• Converted file is present on the file system and has a valid MSThunder-compatible format extension (.mzML, .mzXML, or documented equivalent).
• File integrity check: converted file can be opened and parsed by MSThunder without format errors or corruption.
• Metadata preservation: precursor m/z values, retention times, MS1 and MS2 spectra, and ion mode (positive/negative) are correctly transferred from the original vendor format.
• File size and content comparison: converted file contains expected number and types of spectra relative to the original raw data (no major loss of data during conversion).
• Downstream validation: MSThunder successfully ingests the converted file and produces candidate compound matches without parsing or schema violations.

Limitations

• Current MSThunder version does not support offline processing of raw data; conversion must occur followed by return and analysis of the converted file.
• Conversion workflow is limited to vendors whose raw formats are supported by MSConvert (ThermoFisher, Agilent, and others); unsupported formats will fail conversion.
• Linux environment setup (Ubuntu 20.04 or compatible) and MSConvert installation are prerequisites; platform-specific configuration issues may arise.
• Online processing capability for raw UPLC-HRMS data is under development; alternative workaround is to send raw files to the MSThunder maintainers or upload to Zenodo/GNPS for processing.

Evidence

• [other] Raw data from ThermoFisher, Agilent, and other vendors is processed in a Linux system and converted via MSConvert: "Raw data from ThermoFisher, Agilent, and other vendors is processed in a Linux system and converted via MSConvert, after which the converted file is returned for subsequent analysis"
• [other] Install and configure MSConvert on a Linux system (Ubuntu 20.04 or compatible) and execute conversion targeting MSThunder-compatible output format: "1. Install and configure MSConvert on a Linux system (Ubuntu 20.04 or compatible). 2. Obtain vendor-specific raw data file(s) (ThermoFisher .raw, Agilent .d, or equivalent format). 3. Execute"
• [other] Validate converted file integrity and format compliance before returning for downstream MSThunder analysis: "4. Validate converted file integrity and format compliance. 5. Return the converted file for downstream MSThunder analysis."
• [readme] MSThunder version does not yet support offline processing of raw data; raw data must be processed in Linux and returned as converted file: "Due to environment configuration issues, the current version does not yet support offline processing of raw data."
• [readme] MSThunder is compatible with ThermoFisher, Agilent, and other vendors whose raw data can be converted via MSConvert: "The current version is compatible with ThermoFisher, Agilent, and other vendors whose raw data can be converted via MSConvert."