Reconstruct and Validate Collision Cross Section Reference Library for Labeled Lipids
License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution.
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"
1---2name: lipid-library-curation3description: Use when 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.4license: CC-BY-4.05---67# Reconstruct and Validate Collision Cross Section Reference Library for Labeled Lipids89> **License: restricted** — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. <!-- asb-license-banner -->10## Summary1112Curate 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.1314## When to use1516You 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.1718## When NOT to use1920- 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.21- Your input CCS values are already corrected or bias-adjusted—this skill curates raw reference libraries, not corrected measurements.22- 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.2324## Inputs2526- MobiLipid repository (GitHub clone or ZIP download)27- DTCCS_N2 reference library CSV file (e.g., 'U13C_DT_CCS_library.csv')2829## Outputs3031- Curated and validated CCS library table (CSV or TSV format)32- Library validation report (row counts, CCS range statistics, missing/duplicate flags)3334## How to apply3536Clone 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.3738## Related tools3940- **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/41- **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/MobiLipid4243## Examples4445```46# In R: Load, validate, and export the DTCCS_N2 library47library <- read.csv('U13C_DT_CCS_library.csv')48validated <- library[library$CCS >= 50 & library$CCS <= 300 & !is.na(library$CCS), ]49write.csv(validated, 'U13C_DT_CCS_library_curated.csv', row.names = FALSE)50```5152## Evaluation signals5354- All expected U13C-labeled lipid species (across all lipid classes in the library) are present in the curated table with no missing rows.55- 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).56- No duplicate entries exist for the same lipid species–adduct combination; nomenclature is consistent across all rows.57- Row and column counts match expectations from library documentation; no null or malformed entries remain.58- Curated table successfully imports without type errors or parsing warnings into MobiLipid CCS bias calculation workflow.5960## Limitations6162- Library curation is restricted to U13C-labeled lipids; unlabeled or differently labeled lipids require separate reference libraries.63- 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.64- 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.65- Nomenclature and adduct assignments in measured data must exactly match those in the reference library (e.g., 'PC', '[M+H]') for successful matching.6667## Evidence6869- [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"70- [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)"71- [intro] library_purpose: "Employing a newly established DT CCS N2 library for U13C labeled lipids, which is provided together with the code"72- [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"73- [other] export_step: "Export the curated library table as the canonical output file"
HolobiomicsLab