--- name: linux-command-line-execution description: Use when you have vendor-specific raw mass spectrometry data (ThermoFisher .raw, Agilent . license: CC-BY-4.0 metadata: edam_operation: http://edamontology.org/operation_3434 edam_topics: - http://edamontology.org/topic_3520 - http://edamontology.org/topic_0121 tools: - MSThunder - Ubuntu - MSConvert - Ubuntu 20.04 techniques: - LC-MS derived_from: - doi: 10.1016/j.enceco.2025.07.022 title: MSThunder evidence_spans: - MSThunder provide a deep learning-based nontargeted analytical framework for the accurate and rapid identification of unknown organic pollutants in water - available through our experiments conducted on an Ubuntu 20.04 environment claims: [] provenance: collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2 assembled_by: scripts/collect_metabolomics_collection.py sources: - build: coll_msthunder_cq doi: 10.1016/j.enceco.2025.07.022 title: MSThunder dedup_kept_from: coll_msthunder_cq schema_version: 0.2.0 attribution: generator: AgenticScienceBuilder original_doi: 10.1016/j.enceco.2025.07.022 all_source_dois: - 10.1016/j.enceco.2025.07.022 zenodo_doi: 10.5281/zenodo.20794027 curators: [] promoter: Louis-Félix Nothias sponsor: CNRS & Université Côte d'Azur --- # 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."