HolobiomicsLab 
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<YYYYMMDD_HHMMSS>\Batch Output' subfolder: "Upon completion of the analysis. the generated output will be found in the '\Logger<YYYYMMDD_HHMMSS>\Batch Output' subfolder"
- [readme] The default parameters are provided in \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"