--- name: library-integration-workflow description: Use when you have custom lipid entries (e.g., synthetic lipids, rare natural variants, or isotopically labeled standards) not covered by LipidMatch's default in-silico library, and you want to include them as matching candidates in your UHPLC-HRMS/MS fragment m/z matching workflow without modifying. license: CC-BY-4.0 metadata: edam_operation: http://edamontology.org/operation_3778 edam_topics: - http://edamontology.org/topic_0153 - http://edamontology.org/topic_3375 tools: - LipidMatch - MZmine - XCMS - MS-DIAL - Compound Discoverer derived_from: - doi: 10.1186/s12859-017-1744-3 title: lipidmatch evidence_spans: [] claims: [] provenance: collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v1 assembled_by: scripts/collect_metabolomics_collection.py sources: - build: coll_lipidmatch doi: 10.1186/s12859-017-1744-3 title: lipidmatch dedup_kept_from: coll_lipidmatch schema_version: 0.2.0 --- # library-integration-workflow ## Summary Integration of user-authored .csv lipid libraries into LipidMatch to enable custom lipid entries as matching candidates in subsequent lipidomics analyses. This skill extends LipidMatch's in-silico fragmentation library (>500,000 lipid species across >60 types) with domain-specific or experimental lipid definitions. ## When to use You have custom lipid entries (e.g., synthetic lipids, rare natural variants, or isotopically labeled standards) not covered by LipidMatch's default in-silico library, and you want to include them as matching candidates in your UHPLC-HRMS/MS fragment m/z matching workflow without modifying the core LipidMatch codebase. ## When NOT to use - Your custom lipids are already well-represented in LipidMatch's default in-silico libraries (>500,000 species across >60 types) — direct matching without integration is more efficient. - Your input mass spectrometry data is from Waters instruments — LipidMatch does not currently support Waters files. - You need to modify fragmentation rules or scoring algorithms themselves — this skill integrates pre-defined libraries only; algorithmic changes require developer-level access. ## Inputs - LipidMatch software installation (GarrettLab-UF/LipidMatch from GitHub) - .csv lipid library file with custom lipid entries and annotated m/z fragmentation patterns - MS/MS dataset or synthetic fragment m/z list for validation testing ## Outputs - Registered custom lipid library entries in LipidMatch active library index - Output candidate list from test matching workflow showing custom library entries ranked as matching candidates ## How to apply Obtain the LipidMatch software and manual from the GarrettLab-UF/LipidMatch GitHub repository. Author a test .csv lipid library file conforming to the manual's format specification, including at least 3–5 custom lipid entries with annotated m/z fragmentation patterns. Place the .csv file in the designated library directory within the LipidMatch installation. Run the library integration/loading step (as documented in the manual) to register the custom entries into the active library index. Execute a test matching workflow on a sample MS/MS dataset (or synthetic fragment m/z list) with the integrated library active. Parse and inspect the output candidate list to confirm that custom library entries appear ranked among the matching candidates, validating successful incorporation. ## Related tools - **LipidMatch** (Core software for matching experimental fragment m/z values with simulated library m/z values; accepts integrated user-generated .csv libraries) — https://github.com/GarrettLab-UF/LipidMatch - **MZmine** (Peak picking and feature extraction upstream of LipidMatch matching) - **XCMS** (Peak picking and feature extraction upstream of LipidMatch matching) - **MS-DIAL** (Peak picking and feature extraction upstream of LipidMatch matching) - **Compound Discoverer** (Peak picking and feature extraction upstream of LipidMatch matching) ## Evaluation signals - Custom .csv library file conforms to LipidMatch manual format specification (includes valid lipid structure descriptors and m/z fragmentation patterns). - Library integration/loading step completes without errors in the LipidMatch log or console output. - At least one custom library entry appears in the output candidate list from test matching workflow, ranked by matching score. - Custom entries' m/z values and fragmentation patterns match the input .csv file entries without truncation or corruption. - Test workflow produces deterministic results: re-running with the same integrated library on the same MS/MS dataset yields identical candidate lists. ## Limitations - LipidMatch does not currently support Waters instrument files, limiting integration to data from Q-Exactive, Agilent, Bruker, or SCIEX Q-TOF platforms. - Custom library entries must be manually authored to conform to LipidMatch's .csv format; no automated validation or format conversion tool is provided in the public release. - Integration is file-based; there is no documented GUI or interactive builder for custom library entries — all authoring is manual or script-driven. - No changelog is documented in the README, making version compatibility and library format stability unclear across LipidMatch releases. ## Evidence - [readme] User-generated library integration capability: "LipidMatch allows for facile integration of user generated libraries for unique applications" - [readme] Comprehensive in-silico library baseline: "in-silico fragmentation libraries of over 500,000 lipid species across over 60 lipid types" - [readme] Supported MS platforms for integration: "LipidMatch has been tested and validated using Q-Exactive orbitrap UHPLC-HRMS/MS data obtained from multiple sample types using targeted, data-dependent top-N (ddMS2-topN), and all ion fragmentation" - [readme] Waters platform limitation: "The software does not currently support Waters files" - [other] Workflow task specification: "Run LipidMatch library integration/loading step (as documented in the manual) to register the custom entries into the active library index"