Csv serialization for mass spectrometry

CSV Serialization for Mass Spectrometry

License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. <!-- asb-license-banner -->

Summary

This skill conditionally exports lipid spectral library data to CSV format in two distinct schemas: Excalibur-compatible precursor lists for DDA analysis on Orbitrap instruments, or Skyline-compatible transition lists for targeted proteomics workflows. The choice of schema determines which columns and row structures are serialized, enabling downstream instrument-specific or software-specific analysis.

When to use

Use this skill when you have generated or curated a lipid spectral library (with precursor m/z, adduct information, charge states, retention times, and fragmentation patterns) and need to export it for use in either Excalibur-based DDA experiments on an Orbitrap mass spectrometer, or in Skyline for targeted transition-based workflows. The skill is triggered by a user's explicit format selection (Excalibur or Skyline) and the availability of fully annotated lipid spectral data.

When NOT to use

• Spectral library data has not been fully generated or annotated (missing precursor m/z, charge state, or fragmentation patterns).
• Output is intended for a mass spectrometry software or instrument other than Excalibur or Skyline; use the generic MSP export instead.
• User has not made an explicit format selection or the selection is ambiguous.

Inputs

• Generated lipid spectral library data (in-memory representation with lipid identities, adduct annotations, m/z values, charge states, retention times, and fragmentation patterns)
• User format selection parameter (string: 'Excalibur' or 'Skyline')

Outputs

• CSV file with Excalibur-compatible precursor list (columns: precursor m/z, charge state, retention time; rows: one per lipid-adduct)
• CSV file with Skyline-compatible transition list (columns: precursor m/z, product ion m/z, and transition metadata; rows: one per precursor–product pair)

How to apply

First, accept a format selection parameter from the user (Excalibur or Skyline). Load the generated lipid spectral library data, which must contain precursor m/z values, charge states, retention times, product ion m/z values, and fragmentation metadata for each lipid-adduct combination. For Excalibur format: extract precursor m/z, charge state, and retention time; serialize with Excalibur-required column headers and row structure optimized for DDA on Orbitrap. For Skyline format: extract precursor m/z, product ion m/z values, and transition-specific metadata; serialize with Skyline-required column headers matching the transition list structure. Finally, write the formatted CSV to a file with a naming convention that reflects the selected format. The rationale is that Excalibur and Skyline have incompatible CSV schemas—Excalibur expects precursor-centric rows for DDA scheduling, while Skyline expects precursor-product pairs for targeted methods—so conditional serialization ensures compatibility with the downstream analysis tool.

Related tools

• Excalibur (Target mass spectrometry instrument control and DDA data acquisition software; the Excalibur CSV precursor list schema is the input format for scheduling DDA experiments on Orbitrap instruments)
• Skyline (Targeted proteomics and lipidomics data processing software; the Skyline CSV transition list schema enables import of precursor–product ion pairs for targeted method design and analysis)

Evaluation signals

• For Excalibur output: CSV contains exactly the required columns (precursor m/z, charge state, retention time) with no extra columns; each row corresponds to one unique precursor with consistent numeric formats and charge state notation (+1, +2, etc.)
• For Skyline output: CSV contains precursor m/z and product ion m/z columns; each row represents a single transition; all m/z values are within the expected mass range for the lipid class and adduct type
• CSV file is valid and parseable (no encoding errors, malformed quotes, or inconsistent delimiters); row counts match the expected number of unique precursors (Excalibur) or precursor–product pairs (Skyline)
• Naming convention of the output file reflects the selected format (e.g., '_Excalibur.csv' or '_Skyline.csv')
• Spot-check: manually verify that precursor m/z and retention time values in the CSV match the internal library representation

Limitations

• The skill depends on prior complete generation and annotation of the lipid spectral library; missing or malformed precursor, adduct, or fragmentation data will propagate into the CSV export.
• Excalibur and Skyline CSV schemas are tool-specific and may change with software version updates; users must verify schema compatibility with their installed tool version.
• The skill does not validate or cross-reference m/z values against reference standards or external databases; accuracy is limited by the underlying spectral library generation process and peer-reviewed fragmentation patterns.

Evidence

• [other] accept user format selection (Excalibur or Skyline) as input parameter: "Accept user format selection (Excalibur or Skyline) as input parameter."
• [other] Excalibur format extraction and serialization: "For Excalibur format: extract precursor m/z, charge state, and retention time; serialize as CSV with Excalibur-required column headers and row structure."
• [other] Skyline format extraction and serialization: "For Skyline format: extract precursor m/z, product ion m/z values, and transition-specific metadata; serialize as CSV with Skyline-required column headers and transition list structure."
• [intro] Two distinct export formats available: "Excalibur compatible precursor list (for DDA analysis via orbitrap) or Skylike compatible transition list may be exported by selecting '.CSV'."
• [readme] Lipid spectral library generation with adduct information: "Lipids are generated with respect to class and fatty acid composition, spectra are then generated with respect to their adducts."