--- name: format-conversion-conditional-logic description: Use when you have generated a lipid spectral library (with lipid identities, adducts, m/z values, and fragmentation patterns) and need to export it for downstream mass spectrometry analysis on either an Orbitrap (via Excalibur DDA) or via Skyline's transition-based workflow. license: CC-BY-4.0 metadata: edam_operation: http://edamontology.org/operation_3750 edam_topics: - http://edamontology.org/topic_3520 - http://edamontology.org/topic_0153 tools: - Excalibur - Skyline - LSG techniques: - LC-MS - ion-mobility-MS derived_from: - doi: 10.1021/acs.analchem.2c04518 title: Lipid Spectrum Generator evidence_spans: - Excalibur compatible precursor list (for DDA analysis via orbitrap) claims: [] provenance: collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2 assembled_by: scripts/collect_metabolomics_collection.py sources: - build: coll_lipid_spectrum_generator_cq doi: 10.1021/acs.analchem.2c04518 title: Lipid Spectrum Generator dedup_kept_from: coll_lipid_spectrum_generator_cq schema_version: 0.2.0 attribution: generator: AgenticScienceBuilder original_doi: 10.1021/acs.analchem.2c04518 all_source_dois: - 10.1021/acs.analchem.2c04518 zenodo_doi: 10.5281/zenodo.20794027 curators: [] promoter: Louis-Félix Nothias sponsor: CNRS & Université Côte d'Azur --- # Conditional Format Conversion for Mass Spectrometry Data ## Summary This skill conditionally serializes spectral library data from an in-memory representation into one of two distinct CSV schemas—Excalibur precursor lists for DDA on orbitrap or Skyline transition lists—based on user-selected format. It bridges the gap between a unified spectral library generation pipeline and instrument-specific data requirements. ## When to use You have generated a lipid spectral library (with lipid identities, adducts, m/z values, and fragmentation patterns) and need to export it for downstream mass spectrometry analysis on either an Orbitrap (via Excalibur DDA) or via Skyline's transition-based workflow. Use this skill when the same library must support multiple instrument/software workflows without re-running library generation. ## When NOT to use - Library data is already in MSP (NIST spectral library) format and must remain there; use MSP export instead of conditional CSV conversion. - You need to export to a third instrument platform not supported by Excalibur or Skyline (e.g. SWATH-MS or ion mobility devices); extend the conditional logic first. - Input spectral library has not yet been generated or lacks fragmentation patterns and m/z annotations; complete library generation before attempting format conversion. ## Inputs - In-memory lipid spectral library (lipid identities, adducts, precursor m/z, charge states, retention times, fragmentation patterns) - User-selected format parameter (Excalibur or Skyline) ## Outputs - CSV file in Excalibur-compatible precursor list schema (precursor m/z, charge state, retention time, etc.) - CSV file in Skyline-compatible transition list schema (precursor m/z, product ion m/z, transition metadata, etc.) ## How to apply Prompt the user to select a target format (Excalibur or Skyline) as an input parameter. Load the in-memory spectral library representation containing precursor m/z, charge states, retention times, and fragmentation patterns. For Excalibur format: extract precursor m/z, charge state, and retention time; serialize with Excalibur-required column headers and row structure. For Skyline format: extract precursor m/z, product ion m/z values, and transition-specific metadata; serialize with Skyline-required headers and transition list structure. Write the formatted CSV to file with a naming convention reflecting the selected format. The rationale is that each instrument expects a distinct tabular schema; conditional logic at serialization time avoids maintaining parallel library generation paths. ## Related tools - **Excalibur** (Target instrument software for DDA analysis on orbitrap; defines precursor list CSV schema (precursor m/z, charge state, retention time) consumed by this format.) - **Skyline** (Target software for targeted proteomics/lipidomics; consumes transition list CSV schema (precursor m/z, product ion m/z, transition metadata) generated by this conditional format converter.) - **LSG** (Upstream spectral library generator that produces the in-memory lipid library representation (lipid identities, adducts, m/z, fragmentation patterns) fed into this format conversion skill.) — https://github.com/98104781/LSG/releases/tag/v1.3.0 ## Evaluation signals - CSV file contains all required columns for the selected format: Excalibur (precursor m/z, charge state, retention time) or Skyline (precursor m/z, product ion m/z, transition metadata). - All rows in the output CSV correspond to entries in the source spectral library; no precursor m/z, charge state, or fragment ion values are missing or corrupted. - CSV header row matches the instrument-specific schema (Excalibur or Skyline); a tool-agnostic CSV importer should fail on the wrong schema. - File naming convention reflects the selected format (e.g. '_excalibur.csv' or '_skyline.csv'). - Spot-check: open output CSV in target software (Excalibur or Skyline) without parse errors; precursor/transition counts match library size. ## Limitations - The README does not specify the exact column headers or row structure required by Excalibur and Skyline; implementation must be validated against official schema documentation for each tool. - Conditional logic is binary (Excalibur vs. Skyline); adding support for a third format requires code modification and re-release. - Fragmentation patterns are lossy in CSV format (transition lists flatten spectral peaks); full spectrum information is only preserved in MSP export. - Retention time data may be absent or approximate in early library versions; Skyline transition lists may not include reliable iRT or RT calibration. ## Evidence - [other] User-selected format determines CSV schema: "Accept user format selection (Excalibur or Skyline) as input parameter." - [other] Excalibur format structure: "For Excalibur format: extract precursor m/z, charge state, and retention time; serialize as CSV with Excalibur-required column headers and row structure." - [other] Skyline format structure: "For Skyline format: extract precursor m/z, product ion m/z values, and transition-specific metadata; serialize as CSV with Skyline-required column headers and transition list structure." - [readme] CSV export as alternative to MSP: "Spectral libraries can be exported with the file extension '.MSP' selected. Otherwise, an Excalibur compatible precursor list (for DDA analysis via orbitrap) or Skylike compatible transition list may" - [readme] Instrument-specific use case: "Excalibur compatible precursor list (for DDA analysis via orbitrap)"