--- name: mass-spectrometry-scan-extraction-by-target description: Use when you have raw LC-MS/MS chromatogram files in mzML/mzXML format (converted from Thermo, Waters, or Bruker instruments) acquired in DDA or targeted MS/MS mode, and you need to isolate specific MS1 precursors and their corresponding MS2 fragments based on known m/z values and optional. license: CC-BY-4.0 metadata: edam_operation: http://edamontology.org/operation_3637 edam_topics: - http://edamontology.org/topic_3520 - http://edamontology.org/topic_0121 tools: - meRgeION2 - MergeION2 - GNPS - MassBank - DrugBank techniques: - LC-MS derived_from: - doi: 10.1021/acs.analchem.2c04343 title: MeRgeION evidence_spans: - github.com__daniellyz__meRgeION2 claims: [] provenance: collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2 assembled_by: scripts/collect_metabolomics_collection.py sources: - build: coll_mergeion_cq doi: 10.1021/acs.analchem.2c04343 title: MeRgeION dedup_kept_from: coll_mergeion_cq schema_version: 0.2.0 attribution: generator: AgenticScienceBuilder original_doi: 10.1021/acs.analchem.2c04343 all_source_dois: - 10.1021/acs.analchem.2c04343 zenodo_doi: 10.5281/zenodo.20794027 curators: [] promoter: Louis-Félix Nothias sponsor: CNRS & Université Côte d'Azur --- # Mass spectrometry scan extraction by target ## Summary Extract MS1 and MS2 scans from raw chromatogram files (mzML/mzXML format) by matching user-specified m/z and retention time targets, enabling construction of local spectral libraries without data sharing. This skill is essential for building confidential spectral libraries in metabolomics and pharmaceutical workflows. ## When to use You have raw LC-MS/MS chromatogram files in mzML/mzXML format (converted from Thermo, Waters, or Bruker instruments) acquired in DDA or targeted MS/MS mode, and you need to isolate specific MS1 precursors and their corresponding MS2 fragments based on known m/z values and optional retention time windows to build a local spectral library. ## When NOT to use - Input files are already in processed or library format (e.g., .mgf, .msp, or pre-compiled spectral library) rather than raw chromatogram files - Your workflow requires real-time or streaming analysis of incoming MS data rather than batch extraction from stored files - Chromatogram files are in vendor-proprietary binary formats (.raw, .d) that have not been converted to mzML/mzXML ## Inputs - One or multiple mzML/mzXML chromatogram files converted from Thermo, Waters, or Bruker data files - User-provided m/z targets (numeric list or table) - Optional retention time ranges (min/max in minutes or seconds) - User-provided metadata (compound name, class, provenance) ## Outputs - Extracted MS1 and MS2 scan spectra with metadata (m/z, retention time, scan number, intensity) - GNPS-style spectral library in structured format with combined user-provided metadata - Tabular or structured output file ready for library search and annotation ## How to apply Load one or more mzML/mzXML files using a mass spectrometry data parser compatible with Thermo, Waters, or Bruker formats. Parse user-provided m/z targets and optional retention time ranges into a query specification. Scan the chromatogram data to identify MS1 scans matching the target m/z values within tolerance and retention time bounds. Extract corresponding MS2 fragment spectra for matched precursors. Compile extracted MS1 and MS2 scans into a structured output format with scan metadata (m/z, retention time, scan number, intensity), then merge them into a GNPS-style spectral library combining user-provided metadata. ## Related tools - **MergeION2** (Primary R package for batch extraction of MS1/MS2 scans from mzML/mzXML files, spectral library construction, and library search) — https://github.com/daniellyz/MergeION2 - **GNPS** (Reference spectral library format and public database for library search, annotation, and molecular networking) - **MassBank** (Public reference spectral database for unknown spectrum annotation and compound identification) - **DrugBank** (Public database for drug structure search and annotation during library lookup) ## Examples ``` params.query.sp = list(prec_mz = 369.232, use_prec = T, polarity = "Positive", method = "Cosine", min_frag_match = 6, min_score = 0); search_result = library_query(input_library = library1c, query_spectrum = query.sp, params.query.sp = params.query.sp) ``` ## Evaluation signals - Extracted MS1 scans match the specified m/z targets within the declared tolerance and fall within the provided retention time bounds (if specified) - All extracted MS2 scans are correctly paired to their precursor MS1 scans and contain non-empty fragment ion lists - Output spectral library metadata schema matches GNPS format with all user-provided fields correctly populated - Scan extraction output includes complete metadata columns (m/z, retention time, scan number, intensity) with no null values for successfully extracted scans - Library search using extracted spectra against the pre-compiled GNPS_MASSBANK_PROCESSED_POS_CONSENSUS1 database returns expected compound hits with Cosine similarity ≥ 0.7 for known reference standards ## Limitations - Currently, the pre-compiled spectral database contains only ESI-MS/MS spectra in positive ion mode; negative ion mode data requires alternative reference libraries - Extraction accuracy depends on user-provided m/z precision and retention time bounds; incorrect or overly broad parameters may result in co-eluting contaminant peaks or missed scans - Compatibility is limited to mzML/mzXML formats; vendor proprietary binary formats (.raw, .d, .raw) must be pre-converted by external software (e.g., ProteoWizard) - No changelog available; version and update history tracking is not documented in the repository ## Evidence - [readme] extracting MS1 and MS2 scans from one or multiple raw chromatogram files according to m/z (and retention time) provided by users: "It works by extracting MS1 and MS2 scans from one or multiple raw chromatogram files according to m/z (and retention time) provided by users" - [other] MergeION performs scan extraction by reading mzML/mzXML format files converted from Thermo, Waters, or Bruker instruments and selects MS1 and MS2 scans matching user-specified m/z and optional retention time parameters: "MergeION performs scan extraction by reading one or multiple mzML/mzXML format files converted from Thermo, Water, or Bruker instruments and selects MS1 and MS2 scans matching user-specified m/z and" - [readme] compatible with mzML/mzXML format converted from Thermo, Waters, or Bruker data files in either DDA or targeted MS/MS mode: "It is compatible with mzML/mzXML format converted from Thermo, Water or Bruker data files, in either DDA (Data-driven acquisition) or targeted MS/MS-mode" - [readme] They are then merged into a GNPS-style spectral library combining user-provided metadata: "They are then merged into a GNPS-style spectral library combining user-provided metadata" - [readme] Currently ESI-MS/MS spectra in our collection are all in positive ion mode: "Currently ESI-MS/MS spectra in our collection are all in positive ion mode" - [intro] Building a local high quality spectral library is an essential step in metabolomics and pharmaceutical laboratories, often lacking due to data confidentiality concerns: "Building a local high quality spectral library is an essentiel step thus often lacking in metabolomics and pharmaceutical laboratories. This is often due to the data confidentiality"