lcms-data-format-handling
Summary
Prepare and validate raw LC-MS data in vendor or open formats (mzML, netCDF) for automated peak-picking and downstream processing. This skill ensures data is centroided, of uniform polarity, and properly formatted before routing to algorithm-specific wrappers.
When to use
You have raw LC-MS data from a vendor instrument or in netCDF format and need to ingest it into SLAW or similar untargeted LC-MS workflows. Use this skill when raw data must be converted to mzML, validated for centroiding and polarity uniformity, and prepared for peak-picking dispatch.
When NOT to use
- Input data is already in a standardized, validated feature table or peak matrix format (e.g., CSV with m/z, retention time, intensity columns).
- Data contains a mixture of positive and negative polarity scans in the same file; separate files by polarity first.
- Profile-mode (non-centroided) data cannot be centroided with available vendor tools or ProteoWizard filters.
Inputs
- Raw LC-MS data files (mzML or netCDF format)
- Vendor-supplied MS data (profile or centroided)
- Data polarity metadata (positive or negative)
Outputs
- Centroided mzML files with uniform polarity
- Validated, preprocessed LC-MS data ready for peak-picking
- Polarity classification log (positive/negative detection)
How to apply
Accept raw LC-MS data in mzML or netCDF format and validate that all files are centroided (not profile mode) and of a single polarity (positive or negative only). If profile data is present, use vendor tools (e.g., ProteoWizard with peakPicking filter) to extract centroided data; apply the filter peakPicking vendor msLevel=1-2 to retain only vendor-provided centroids and discard low-confidence peaks. Verify that MS1 and optional DDA-MS2 scans are present and that DIA-MS data is not included (not supported). Standardize all input files to mzML format with consistent naming. Log or extract the detected polarity from at least one representative file to confirm uniformity across the batch. Output the validated, centroided mzML files ready for the peak-picking routing stage.
Related tools
- ProteoWizard (Convert vendor raw data to centroided mzML; apply peakPicking vendor filter to extract MS1-2 centroids)
- SLAW (Downstream workflow that ingests validated mzML files and routes them to Centwave, FeatureFinderMetabo, or ADAP peak pickers) — https://github.com/zamboni-lab/SLAW
Examples
# Using ProteoWizard to convert and centroid raw data to mzML
msConvert vendor_raw_data.raw --mzML --filter "peakPicking vendor msLevel=1-2" --outdir ./mzml_output/
# Validate and stage centroided files in SLAW input folder for peak-picking dispatch
Evaluation signals
- All output mzML files are readable by peak-picking tools (Centwave, FeatureFinderMetabo, ADAP) without errors.
- Data contains only centroided peaks; no profile-mode scans remain.
- All files in a batch share a single polarity (positive or negative); no mixed-polarity files are present.
- MS1 and (optional) MS2 scans are retained; DIA-MS scans are absent or flagged separately.
- File headers and metadata (mzML schema, polarity flags) validate against SLAW input schema.
Limitations
- DIA-MS data is not supported by SLAW; files with DIA-only MS2 must be excluded or flagged separately.
- Profile-mode data cannot be converted to centroided format after acquisition; vendor tools must be applied at conversion time.
- Mixed-polarity files must be split into separate positive and negative mzML files before processing; no within-file demultiplexing is performed.
- Low-abundance centroids removed during preprocessing may reduce feature detection sensitivity; archival of unfiltered raw data is recommended.
Evidence
- [readme] Raw MS data in mzML format. Files can include MS1 and DDA-MS2 scans. DIA-MS is not supported. All data must be centroided and of unique polarity.: "Raw MS data in mzML format. Files can include MS1 and DDA-MS2 scans. DIA-MS is not supported. All data must be centroided and of unique polarity."
- [readme] Centroided mzML can be obtained with ProteoWizard. Discard all profile data and always prioritize the centroid data provided by vendor's software, e.g. with the filter
peakPicking vendor msLevel=1-2.: "Centroided mzML can be obtained with ProteoWizard. Discard all profile data and always prioritize the centroid data provided by vendor's software, e.g. with the filter `peakPicking vendor"
- [other] Accept a configuration specification naming the target peak-picking algorithm (Centwave, FeatureFinderMetabo, or ADAP) and raw LC-MS data (mzML or netCDF format).: "Accept a configuration specification naming the target peak-picking algorithm (Centwave, FeatureFinderMetabo, or ADAP) and raw LC-MS data (mzML or netCDF format)."
- [readme] Guessing polarity from file:DDA1.mzML ... Polarity detected: positive: "Guessing polarity from file:DDA1.mzML ... Polarity detected: positive"
1---2name: lcms-data-format-handling3description: Use when you have raw LC-MS data from a vendor instrument or in netCDF format and need to ingest it into SLAW or similar untargeted LC-MS workflows. Use this skill when raw data must be converted to mzML, validated for centroiding and polarity uniformity, and prepared for peak-picking dispatch.4license: CC-BY-4.05---67# lcms-data-format-handling89## Summary1011Prepare and validate raw LC-MS data in vendor or open formats (mzML, netCDF) for automated peak-picking and downstream processing. This skill ensures data is centroided, of uniform polarity, and properly formatted before routing to algorithm-specific wrappers.1213## When to use1415You have raw LC-MS data from a vendor instrument or in netCDF format and need to ingest it into SLAW or similar untargeted LC-MS workflows. Use this skill when raw data must be converted to mzML, validated for centroiding and polarity uniformity, and prepared for peak-picking dispatch.1617## When NOT to use1819- Input data is already in a standardized, validated feature table or peak matrix format (e.g., CSV with m/z, retention time, intensity columns).20- Data contains a mixture of positive and negative polarity scans in the same file; separate files by polarity first.21- Profile-mode (non-centroided) data cannot be centroided with available vendor tools or ProteoWizard filters.2223## Inputs2425- Raw LC-MS data files (mzML or netCDF format)26- Vendor-supplied MS data (profile or centroided)27- Data polarity metadata (positive or negative)2829## Outputs3031- Centroided mzML files with uniform polarity32- Validated, preprocessed LC-MS data ready for peak-picking33- Polarity classification log (positive/negative detection)3435## How to apply3637Accept raw LC-MS data in mzML or netCDF format and validate that all files are centroided (not profile mode) and of a single polarity (positive or negative only). If profile data is present, use vendor tools (e.g., ProteoWizard with peakPicking filter) to extract centroided data; apply the filter `peakPicking vendor msLevel=1-2` to retain only vendor-provided centroids and discard low-confidence peaks. Verify that MS1 and optional DDA-MS2 scans are present and that DIA-MS data is not included (not supported). Standardize all input files to mzML format with consistent naming. Log or extract the detected polarity from at least one representative file to confirm uniformity across the batch. Output the validated, centroided mzML files ready for the peak-picking routing stage.3839## Related tools4041- **ProteoWizard** (Convert vendor raw data to centroided mzML; apply peakPicking vendor filter to extract MS1-2 centroids)42- **SLAW** (Downstream workflow that ingests validated mzML files and routes them to Centwave, FeatureFinderMetabo, or ADAP peak pickers) — https://github.com/zamboni-lab/SLAW4344## Examples4546```47# Using ProteoWizard to convert and centroid raw data to mzML48msConvert vendor_raw_data.raw --mzML --filter "peakPicking vendor msLevel=1-2" --outdir ./mzml_output/49# Validate and stage centroided files in SLAW input folder for peak-picking dispatch50```5152## Evaluation signals5354- All output mzML files are readable by peak-picking tools (Centwave, FeatureFinderMetabo, ADAP) without errors.55- Data contains only centroided peaks; no profile-mode scans remain.56- All files in a batch share a single polarity (positive or negative); no mixed-polarity files are present.57- MS1 and (optional) MS2 scans are retained; DIA-MS scans are absent or flagged separately.58- File headers and metadata (mzML schema, polarity flags) validate against SLAW input schema.5960## Limitations6162- DIA-MS data is not supported by SLAW; files with DIA-only MS2 must be excluded or flagged separately.63- Profile-mode data cannot be converted to centroided format after acquisition; vendor tools must be applied at conversion time.64- Mixed-polarity files must be split into separate positive and negative mzML files before processing; no within-file demultiplexing is performed.65- Low-abundance centroids removed during preprocessing may reduce feature detection sensitivity; archival of unfiltered raw data is recommended.6667## Evidence6869- [readme] Raw MS data in mzML format. Files can include MS1 and DDA-MS2 scans. DIA-MS is not supported. **All data must be centroided and of unique polarity**.: "Raw MS data in mzML format. Files can include MS1 and DDA-MS2 scans. DIA-MS is not supported. **All data must be centroided and of unique polarity**."70- [readme] Centroided mzML can be obtained with ProteoWizard. Discard all profile data and always prioritize the centroid data provided by vendor's software, e.g. with the filter `peakPicking vendor msLevel=1-2`.: "Centroided mzML can be obtained with ProteoWizard. Discard all profile data and always prioritize the centroid data provided by vendor's software, e.g. with the filter `peakPicking vendor"71- [other] Accept a configuration specification naming the target peak-picking algorithm (Centwave, FeatureFinderMetabo, or ADAP) and raw LC-MS data (mzML or netCDF format).: "Accept a configuration specification naming the target peak-picking algorithm (Centwave, FeatureFinderMetabo, or ADAP) and raw LC-MS data (mzML or netCDF format)."72- [readme] Guessing polarity from file:DDA1.mzML ... Polarity detected: positive: "Guessing polarity from file:DDA1.mzML ... Polarity detected: positive"
HolobiomicsLab 