--- name: high-resolution-ms2-peak-assignment description: Use when you have high-resolution MS2 data in .ms2 format from lipid A samples and need to perform automated structure annotation to identify lipid A molecular variants and their fragmentation patterns at scale. license: CC-BY-4.0 metadata: edam_operation: http://edamontology.org/operation_3647 edam_topics: - http://edamontology.org/topic_0153 - http://edamontology.org/topic_3520 tools: - Python - git - MSConvert (ProteoWizard) techniques: - LC-MS derived_from: - doi: 10.1021/acs.analchem.5c00520 title: LipidA-IDER evidence_spans: - $ python LipidAIDER_GUI.py - 'Step 0: Install git (if you have not done so before)' claims: [] provenance: collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2 assembled_by: scripts/collect_metabolomics_collection.py sources: - build: coll_lipida_ider_cq doi: 10.1021/acs.analchem.5c00520 title: LipidA-IDER dedup_kept_from: coll_lipida_ider_cq schema_version: 0.2.0 attribution: generator: AgenticScienceBuilder original_doi: 10.1021/acs.analchem.5c00520 all_source_dois: - 10.1021/acs.analchem.5c00520 zenodo_doi: 10.5281/zenodo.20794027 curators: [] promoter: Louis-Félix Nothias sponsor: CNRS & Université Côte d'Azur --- # high-resolution-ms2-peak-assignment ## Summary Automated structure annotation of lipid A from high-resolution tandem mass spectrometry (MS2) data by assigning fragment peaks to lipid A structural moieties. This skill is essential when you have MS2 spectra and need to identify and annotate lipid A molecular structures at systems level. ## When to use Apply this skill when you have high-resolution MS2 data in .ms2 format from lipid A samples and need to perform automated structure annotation to identify lipid A molecular variants and their fragmentation patterns at scale. ## When NOT to use - Input data is not in .ms2 format — first convert using MSConvert (ProteoWizard) with Peak Picking (CWT algorithm) and MS Level 2 filters - Your mass spectrometry data is from non-lipid A samples or low-resolution instruments not suitable for structure annotation - You are running on MacOS or Linux — LipidA-IDER has only been tested on Windows; use on other platforms has not been validated ## Inputs - .ms2 format mass spectrometry data files - LipidAIDER_AnalysisParam.csv parameter settings file - LipidAIDER_BatchAnalysisFiles.csv batch specification (for CLI mode) ## Outputs - Annotated lipid A structure assignments - Fragment peak annotations with m/z assignments - Batch output folder (Logger//Batch Output) ## How to apply LipidA-IDER performs peak assignment by accepting .ms2 format input files containing high-resolution tandem mass spectrometry data. The tool uses configurable analysis parameters (stored in LipidAIDER_AnalysisParam.csv) to control peak picking, m/z tolerance, and structural annotation thresholds. Users prepare input files and parameter settings, then execute the analysis via either GUI (python LipidAIDER_GUI.py) or CLI (python LIPIDAIDER_main.py). The analysis generates annotated output in a timestamped Logger directory containing structural assignments for detected lipid A species. Success is verified by confirming that annotated lipid A structure outputs are generated and saved to the specified output directory with assigned fragment annotations. ## Related tools - **Python** (Execution environment for LipidA-IDER GUI and CLI interfaces) - **git** (Repository cloning tool to obtain LipidA-IDER source code) — https://github.com/Systems-Biology-Of-Lipid-Metabolism-Lab/LipidA-IDER - **MSConvert (ProteoWizard)** (Data format conversion to .ms2 with peak picking (CWT algorithm, MS Level 2)) — https://proteowizard.sourceforge.io/download.html ## Examples ``` $ python LIPIDAIDER_main.py -m /path/to/demo_input_files/sample.ms2 ``` ## Evaluation signals - Output files are generated in the timestamped Logger directory with expected structure (Logger//Batch Output) - Annotated lipid A structural assignments are present in output with fragment peak m/z values assigned - No runtime errors or warnings in terminal/CLI output indicating parameter or data format issues - Output files contain expected number of annotated lipid A species matching input sample count - Batch Output folder contains dated subdirectory matching analysis run timestamp ## Limitations - LipidA-IDER has only been tested on Windows; use on MacOS and Linux has not been tested - Currently accepts only .ms2 format data files; other formats require preprocessing with MSConvert - Requires .ms2 input files to have been processed with Peak Picking using CWT algorithm at MS Level 2 - Performance and accuracy depend on appropriate parameter tuning in LipidAIDER_AnalysisParam.csv for the specific MS data nature ## Evidence - [readme] LipidA-IDER is an automated structure annotation tool for systems-level scale identification of lipid A from high resolution tandem mass spectrometry (MS2) data: "LipidA-IDER is an automated structure annotation tool for systems-level scale identification of lipid A from high resolution tandem mass spectrometry (MS2) data" - [readme] LipidAIDER currently accepts data in .ms2 format. To convert to .ms2, use MSConvert (ProteoWizard) (download from: https://proteowizard.sourceforge.io/download.html) Settings: Output format: .ms2, Filters: Peak Picking, Algorithm: CWT, MS Levels: 2: "LipidAIDER currently accepts data in .ms2 format. To convert to .ms2, use MSConvert (ProteoWizard) Settings: Output format: .ms2, Filters: Peak Picking, Algorithm: CWT, MS Levels: 2" - [readme] As of current, LipidA-IDER has only been tested on Windows. Use of LipidA-IDER on MacOS and Linux has *not* been tested: "LipidA-IDER has only been tested on Windows. Use of LipidA-IDER on MacOS and Linux has *not* been tested" - [readme] Upon completion of the analysis. the generated output will be found in the '\Logger\\Batch Output' subfolder: "Upon completion of the analysis. the generated output will be found in the '\Logger\\Batch Output' subfolder" - [readme] The default parameters are provided in [\Settings\LipidAIDER_AnalysisParam.csv](/Settings/LipidAIDER_AnalysisParam.csv). Users may edit this file to according to the nature of their data: "Users may edit this file to according to the nature of their data"