precursor-list-formatting-for-dda
License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution.
Summary
Convert a generated lipid spectral library into an Excalibur-compatible precursor list CSV format suitable for data-dependent acquisition (DDA) analysis on an Orbitrap mass spectrometer. This skill conditionally serializes precursor m/z, charge state, and retention time metadata into the column structure and row format required by Excalibur.
When to use
Apply this skill when you have generated a lipid spectral library (lipid identities, adducts, m/z values, fragmentation patterns) and your downstream analysis requires DDA acquisition on an Orbitrap instrument using Excalibur software. Use this instead of MSP export when you need a precursor inclusion list rather than a full spectral library.
When NOT to use
- Input is an MSP format spectral library — export MSP directly instead of converting to precursor list.
- Downstream analysis uses targeted MRM or SRM on a triple-quadrupole instrument — use Skyline-compatible transition list format instead.
- User requires full fragmentation spectra rather than precursor targeting — use MSP export.
Inputs
- Generated lipid spectral library data (in-memory representation: lipid identities, adducts, precursor m/z, charge states, retention times, fragmentation patterns)
- User format selection parameter (string: 'Excalibur' or 'Skyline')
Outputs
- Excalibur-compatible precursor list CSV file (with Excalibur-required column headers, one precursor per row)
How to apply
Accept a user-facing format selection parameter (Excalibur vs. Skyline) and route to the Excalibur branch. Load the generated lipid spectral library data, extracting precursor m/z values, charge states, and retention time metadata for each lipid–adduct combination. Serialize these fields into a CSV file with Excalibur-required column headers and row structure (as defined by Excalibur's precursor list schema). Write the formatted CSV to disk with a naming convention reflecting the selected format. The rationale is that Orbitrap DDA relies on precursor inclusion lists to target specific m/z and charge combinations; Excalibur's format specification ensures the instrument and software can parse and apply these targets correctly.
Related tools
- Excalibur (Target mass spectrometer and acquisition software for which the precursor list CSV is formatted; interprets the serialized precursor m/z, charge, and RT to configure DDA inclusion lists on Orbitrap instruments)
- LSG (Upstream tool that generates the lipid spectral library data and provides the conditional CSV export mechanism (including the Excalibur branch)) — https://github.com/98104781/LSG
Evaluation signals
- CSV file is valid and parseable (no malformed rows, consistent column count per row)
- CSV column headers match Excalibur's required schema (e.g., precursor m/z, charge state, retention time fields are present and named correctly)
- All precursor m/z values are numeric, positive, and within the expected range for lipids (typically 300–1200 m/z)
- Charge states are positive integers (typically +1, +2, +3, or +4 for lipid adducts)
- File naming convention reflects 'Excalibur' format selection (e.g., includes 'Excalibur' or '.csv' extension)
Limitations
- Fragmentation patterns are not included in the precursor list CSV; if fragment masses are needed for method development, export MSP format instead.
- Retention time values depend on prior annotation or prediction in the spectral library generation step; missing or inaccurate RTs will reduce targeting precision.
- Excalibur format is specific to Orbitrap instruments; users with different mass spectrometer platforms should select the appropriate export format.
- User must manually select the correct format (Excalibur vs. Skyline); no automatic detection of downstream instrument type.
Evidence
- [other] For Excalibur format: extract precursor m/z, charge state, and retention time; serialize as CSV with Excalibur-required column headers and row structure.: "For Excalibur format: extract precursor m/z, charge state, and retention time; serialize as CSV with Excalibur-required column headers and row structure."
- [other] LSG implements a conditional CSV export mechanism that generates either an Excalibur-compatible precursor list for DDA analysis via orbitrap or a Skyline-compatible transition list, selected by the user.: "LSG implements a conditional CSV export mechanism that generates either an Excalibur-compatible precursor list for DDA analysis via orbitrap or a Skyline-compatible transition list, selected by the"
- [readme] Otherwise, an Excalibur compatible precursor list (for DDA analysis via orbitrap) or Skylike compatible transition list may be exported by selecting '.CSV'.: "Otherwise, an Excalibur compatible precursor list (for DDA analysis via orbitrap) or Skylike compatible transition list may be exported by selecting '.CSV'."
- [readme] Lipids are generated with respect to class and fatty acid composition, spectra are then generated with respect to their adducts.: "Lipids are generated with respect to class and fatty acid composition, spectra are then generated with respect to their adducts."
- [other] Accept user format selection (Excalibur or Skyline) as input parameter.: "Accept user format selection (Excalibur or Skyline) as input parameter."
1---2name: precursor-list-formatting-for-dda-23description: Use when you have generated a lipid spectral library (lipid identities, adducts, m/z values, fragmentation patterns) and your downstream analysis requires DDA acquisition on an Orbitrap instrument using Excalibur software.4license: CC-BY-4.05---67# precursor-list-formatting-for-dda89> **License: restricted** — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. <!-- asb-license-banner -->10## Summary1112Convert a generated lipid spectral library into an Excalibur-compatible precursor list CSV format suitable for data-dependent acquisition (DDA) analysis on an Orbitrap mass spectrometer. This skill conditionally serializes precursor m/z, charge state, and retention time metadata into the column structure and row format required by Excalibur.1314## When to use1516Apply this skill when you have generated a lipid spectral library (lipid identities, adducts, m/z values, fragmentation patterns) and your downstream analysis requires DDA acquisition on an Orbitrap instrument using Excalibur software. Use this instead of MSP export when you need a precursor inclusion list rather than a full spectral library.1718## When NOT to use1920- Input is an MSP format spectral library — export MSP directly instead of converting to precursor list.21- Downstream analysis uses targeted MRM or SRM on a triple-quadrupole instrument — use Skyline-compatible transition list format instead.22- User requires full fragmentation spectra rather than precursor targeting — use MSP export.2324## Inputs2526- Generated lipid spectral library data (in-memory representation: lipid identities, adducts, precursor m/z, charge states, retention times, fragmentation patterns)27- User format selection parameter (string: 'Excalibur' or 'Skyline')2829## Outputs3031- Excalibur-compatible precursor list CSV file (with Excalibur-required column headers, one precursor per row)3233## How to apply3435Accept a user-facing format selection parameter (Excalibur vs. Skyline) and route to the Excalibur branch. Load the generated lipid spectral library data, extracting precursor m/z values, charge states, and retention time metadata for each lipid–adduct combination. Serialize these fields into a CSV file with Excalibur-required column headers and row structure (as defined by Excalibur's precursor list schema). Write the formatted CSV to disk with a naming convention reflecting the selected format. The rationale is that Orbitrap DDA relies on precursor inclusion lists to target specific m/z and charge combinations; Excalibur's format specification ensures the instrument and software can parse and apply these targets correctly.3637## Related tools3839- **Excalibur** (Target mass spectrometer and acquisition software for which the precursor list CSV is formatted; interprets the serialized precursor m/z, charge, and RT to configure DDA inclusion lists on Orbitrap instruments)40- **LSG** (Upstream tool that generates the lipid spectral library data and provides the conditional CSV export mechanism (including the Excalibur branch)) — https://github.com/98104781/LSG4142## Evaluation signals4344- CSV file is valid and parseable (no malformed rows, consistent column count per row)45- CSV column headers match Excalibur's required schema (e.g., precursor m/z, charge state, retention time fields are present and named correctly)46- All precursor m/z values are numeric, positive, and within the expected range for lipids (typically 300–1200 m/z)47- Charge states are positive integers (typically +1, +2, +3, or +4 for lipid adducts)48- File naming convention reflects 'Excalibur' format selection (e.g., includes 'Excalibur' or '.csv' extension)4950## Limitations5152- Fragmentation patterns are not included in the precursor list CSV; if fragment masses are needed for method development, export MSP format instead.53- Retention time values depend on prior annotation or prediction in the spectral library generation step; missing or inaccurate RTs will reduce targeting precision.54- Excalibur format is specific to Orbitrap instruments; users with different mass spectrometer platforms should select the appropriate export format.55- User must manually select the correct format (Excalibur vs. Skyline); no automatic detection of downstream instrument type.5657## Evidence5859- [other] For Excalibur format: extract precursor m/z, charge state, and retention time; serialize as CSV with Excalibur-required column headers and row structure.: "For Excalibur format: extract precursor m/z, charge state, and retention time; serialize as CSV with Excalibur-required column headers and row structure."60- [other] LSG implements a conditional CSV export mechanism that generates either an Excalibur-compatible precursor list for DDA analysis via orbitrap or a Skyline-compatible transition list, selected by the user.: "LSG implements a conditional CSV export mechanism that generates either an Excalibur-compatible precursor list for DDA analysis via orbitrap or a Skyline-compatible transition list, selected by the"61- [readme] Otherwise, an Excalibur compatible precursor list (for DDA analysis via orbitrap) or Skylike compatible transition list may be exported by selecting '.CSV'.: "Otherwise, an Excalibur compatible precursor list (for DDA analysis via orbitrap) or Skylike compatible transition list may be exported by selecting '.CSV'."62- [readme] Lipids are generated with respect to class and fatty acid composition, spectra are then generated with respect to their adducts.: "Lipids are generated with respect to class and fatty acid composition, spectra are then generated with respect to their adducts."63- [other] Accept user format selection (Excalibur or Skyline) as input parameter.: "Accept user format selection (Excalibur or Skyline) as input parameter."
HolobiomicsLab