# Tandem Mass Spectrometry Data Interpretation > Use when you have high-resolution MS2 data (.ms2 format) from tandem mass spectrometry analysis of lipid A-containing samples and need to perform automated structure annotation and identification at systems scale. - Skill: `holobiomicslab/tandem-mass-spectrometry-data-interpretation` (Agent Skill) - Install (CLI): `npx skillmds@latest add holobiomicslab/tandem-mass-spectrometry-data-interpretation` - Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/tandem-mass-spectrometry-data-interpretation/raw - Safety review: PASS (external: skill-scanner PASS, skillspector PASS) - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Coding & Dev Tools - License: CC-BY-4.0 - Author: HolobiomicsLab (https://skillmd.com/u/holobiomicslab) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/holobiomicslab/tandem-mass-spectrometry-data-interpretation --- # tandem-mass-spectrometry-data-interpretation ## Summary Automated structure annotation of lipid A from high-resolution tandem mass spectrometry (MS2) data using LipidA-IDER, an open-source tool that identifies and classifies lipid A molecular species at systems scale. This skill enables conversion of raw MS2 spectral data into annotated lipid structure outputs. ## When to use You have high-resolution MS2 data (.ms2 format) from tandem mass spectrometry analysis of lipid A-containing samples and need to perform automated structure annotation and identification at systems scale. You lack established lipid A reference libraries or wish to standardize annotation across large sample batches. You want to avoid manual peak assignment and structural hypothesis generation. ## When NOT to use - Input data is in formats other than .ms2 (e.g., raw vendor formats, mzML, NetCDF) without prior conversion - Running on MacOS or Linux systems, as LipidA-IDER has only been tested and validated on Windows - Data consists of MS1 spectra only or does not include tandem MS2 fragmentation data ## Inputs - .ms2 format mass spectrometry data files - LipidAIDER_AnalysisParam.csv configuration file (optional custom parameters) - LipidAIDER_BatchAnalysisFiles.csv batch definition file (for CLI mode) ## Outputs - Annotated lipid A structure assignments - Batch output files in Logger//Batch Output directory - Per-spectrum annotation records with lipid A molecular identities ## How to apply First, prepare input data by converting raw mass spectrometry files to .ms2 format using MSConvert (ProteoWizard) with peak picking (CWT algorithm) and MS level 2 filtering. Clone the LipidA-IDER repository and install Python dependencies. Configure analysis parameters in the LipidAIDER_AnalysisParam.csv settings file to match your data characteristics (e.g., m/z accuracy, fragment ion thresholds). Execute LipidA-IDER via either the GUI ($ python LipidAIDER_GUI.py) for interactive file selection and parameter adjustment, or CLI ($ python LIPIDAIDER_main.py -m ) for batch processing. Monitor the Logger directory for timestamped output folders containing annotated lipid structures. Verify output completeness by checking that all input .ms2 records generated corresponding structure annotations. ## Related tools - **MSConvert (ProteoWizard)** (Converts raw mass spectrometry data to .ms2 format with peak picking and MS level 2 filtering) — https://proteowizard.sourceforge.io/download.html - **Python** (Runtime environment for executing LipidA-IDER GUI and CLI interfaces) - **git** (Version control tool for cloning the LipidA-IDER repository) ## Examples ``` $ python LIPIDAIDER_main.py -m /path/to/sample.ms2 ``` ## Evaluation signals - Output directory exists in Logger with correctly formatted YYYYMMDD_HHMMSS timestamp - Batch Output folder contains annotation records for all input .ms2 files without truncation or errors - Annotated lipid A structures include defined molecular identities with m/z values and fragment ion assignments consistent with input spectra - Parameter values in settings file align with expected MS data characteristics (e.g., instrument resolution, ion mode) - No error logs or warnings in stdout/stderr indicating failed spectrum processing or missing required input files ## Limitations - LipidA-IDER has only been tested on Windows; use on MacOS and Linux has not been tested and is unsupported - Accepts only .ms2 format input; conversion from other formats (raw vendor data, mzML) is required beforehand - Output quality and annotation accuracy depend on proper configuration of analysis parameters in LipidAIDER_AnalysisParam.csv; misaligned parameters may produce spurious or incomplete annotations - Tool is optimized for lipid A structures specifically; applicability to other lipid classes or modified lipid A species is not documented ## 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] As of current, LipidA-IDER has only been tested on Windows. Use of LipidA-IDER on MacOS and Linux has *not* been tested.: "As of current, LipidA-IDER has only been tested on Windows. Use of LipidA-IDER on MacOS and Linux has *not* been tested." - [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] 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] In the event that you do not have initial .ms2 data, we have provided the some demo input files for your use here: [\Source\demo_input_files]: "In the event that you do not have initial .ms2 data, we have provided the some demo input files for your use"