Lipid library curation

Reconstruct and Validate Collision Cross Section Reference Library for Labeled Lipids

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Summary

Curate and validate a structured collision cross section (CCS) reference library for isotope-labeled lipids (e.g., U13C) by extracting, parsing, and quality-checking CCS values from a distributed package. This skill ensures the library meets physical and structural constraints required for downstream CCS bias assessment in ion mobility–mass spectrometry (IM-MS) lipidomics.

When to use

You have obtained MobiLipid or a similar IM-MS lipidomics package that bundles a CCS reference library for labeled lipids, and you need to verify library integrity, validate that all expected lipid species are present with plausible numeric CCS values, and prepare a canonical curated version for use in CCS bias correction workflows.

When NOT to use

• You are using a non-isotope-labeled lipid CCS library or a library not bundled with MobiLipid—this skill is specific to U13C-labeled reference libraries.
• Your input CCS values are already corrected or bias-adjusted—this skill curates raw reference libraries, not corrected measurements.
• You need only to run CCS bias correction on already-measured data without verifying the library itself—use the provided library file directly if trust in the distributor is sufficient.

Inputs

• MobiLipid repository (GitHub clone or ZIP download)
• DTCCS_N2 reference library CSV file (e.g., 'U13C_DT_CCS_library.csv')

Outputs

• Curated and validated CCS library table (CSV or TSV format)
• Library validation report (row counts, CCS range statistics, missing/duplicate flags)

How to apply

Clone or download the MobiLipid repository and locate the DTCCS_N2 reference library file (e.g., 'U13C_DT_CCS_library.csv'). Parse the CSV into a structured table with columns for lipid class, lipid species identifier, and CCS reference value. Validate that all U13C-labeled lipid entries expected in the library are present, that CCS values are numeric, and that they fall within physically plausible ranges (typically 50–300 Ų for small lipids). Check for missing values, duplicates, and nomenclature consistency. Export the validated table as a canonical output file (CSV or TSV) for use as input to CCS bias calculation and correction steps in the MobiLipid workflow.

Related tools

• R (Scripting language for parsing, validating, and exporting the library table; commonly used to check data types, ranges, and completeness) — https://cran.r-project.org/
• MobiLipid (Parent tool that bundles the DTCCS_N2 library; curated library is consumed by MobiLipid's CCS bias calculation and correction workflows) — https://github.com/FelinaHildebrand/MobiLipid

Examples

# In R: Load, validate, and export the DTCCS_N2 library
library <- read.csv('U13C_DT_CCS_library.csv')
validated <- library[library$CCS >= 50 & library$CCS <= 300 & !is.na(library$CCS), ]
write.csv(validated, 'U13C_DT_CCS_library_curated.csv', row.names = FALSE)

Evaluation signals

• All expected U13C-labeled lipid species (across all lipid classes in the library) are present in the curated table with no missing rows.
• All CCS values are numeric and fall within the physically plausible range of 50–300 Ų (or appropriate range for the lipid size and charge state being studied).
• No duplicate entries exist for the same lipid species–adduct combination; nomenclature is consistent across all rows.
• Row and column counts match expectations from library documentation; no null or malformed entries remain.
• Curated table successfully imports without type errors or parsing warnings into MobiLipid CCS bias calculation workflow.

Limitations

• Library curation is restricted to U13C-labeled lipids; unlabeled or differently labeled lipids require separate reference libraries.
• CCS values are valid only for nitrogen (N2) drift gas at the conditions specified in the DTCCS_N2 library; values are not transferable to other drift gases or instruments without recalibration.
• CCS correction functions in MobiLipid require a minimum of 3 lipids per lipid class–adduct combination, so lipid classes with fewer detected U13C standards may not support bias correction.
• Nomenclature and adduct assignments in measured data must exactly match those in the reference library (e.g., 'PC', '[M+H]') for successful matching.

Evidence

• [readme] library_file_location: "the .csv file of the DT CCS N2 library for U13C labeled lipids of yeast ('U13C_DT_CCS_library.csv') is downloaded"
• [other] validation_range_check: "Validate that all U13C labeled lipid entries are present and CCS values are numeric and within physically plausible ranges (typically 50–300 Ų for small lipids)"
• [intro] library_purpose: "Employing a newly established DT CCS N2 library for U13C labeled lipids, which is provided together with the code"
• [other] parsing_structure: "Parse the library data into a structured table format (CSV or TSV) containing lipid class, lipid species identifier, and CCS reference value columns"
• [other] export_step: "Export the curated library table as the canonical output file"