rgoslin

Workflows

Standard Workflow

The R implementation for the Grammar of Succint Lipid Nomenclature parses different shorthand notation dialects for lipid names, normalizes them, and calculates chemical properties.

library(rgoslin)

# Check which grammars are supported
listAvailableGrammars()

# Check whether a given lipid name can be parsed
isValidLipidName("PC 32:1")

# Parse a single lipid name to return a data frame of properties
df <- parseLipidNames("PC 32:1")

# Parse a lipid name with a manually specified grammar
tagDf <- parseLipidNames("TG(16:1(5E)/18:0/20:2(3Z,6Z))", grammar = "LipidMaps")

# Parse multiple lipid names using a vector
multipleLipidNamesDf <- parseLipidNames(c("PC 32:1", "LPC 34:1", "TG(18:1_18:0_16:1)"))

Input: A character vector of lipid shorthand names. Output: A data frame containing parsed lipid properties (e.g., normalized name, mass, sum formula, category).

When to Use

• Parsing shorthand lipid names into structural representations using parseLipidNames().
• Validating if a lipid name is compliant with supported grammars using isValidLipidName().
• Retrieving calculated monoisotopic masses, sum formulas, and LIPID MAPS categories for parsed lipids.
• Converting IUPAC-compliant fatty acid names to updated shorthand nomenclature using parseLipidNames(..., grammar = "FattyAcids").

When NOT to Use

• For general mass spectrometry raw data processing or peak picking; use xcms instead.
• For handling raw MSn spectra or chromatograms; use MSnbase or Spectra instead.

Data Requirements

• Input data must be a character vector of lipid names (e.g., "PC 32:1", "TG(16:1(5E)/18:0/20:2(3Z,6Z))").
• Supported grammars include "Shorthand2020", "Goslin", "FattyAcids", "LipidMaps", "SwissLipids", and "HMDB".

Key Parameters

• grammar (NULL): The specific grammar to parse against (e.g., "Goslin", "LipidMaps", "FattyAcids"). If omitted, all available parsers are tested sequentially.

Best Practices

• Use listAvailableGrammars() to check supported grammars before parsing.
• Explicitly specify the grammar parameter in parseLipidNames() when parsing large vectors to avoid testing all parsers and improve performance.
• Use isValidLipidName() to quickly filter out unparseable names before running full parsing.

Common Pitfalls

• Omitting the grammar argument on large datasets: Causes slow execution because all grammars are tested sequentially. Fix: Specify grammar = "Goslin" or another specific grammar.
• Parsing names with unsupported suffixes (like isotopic labels like (d9)): Causes parsing errors. Fix: Preprocess names using string manipulation (e.g., str_match or str_replace_all) to remove or convert suffixes before parsing.

Alternatives

• lipidr: For downstream analysis, visualization, and QC of lipidomics data (can be integrated with rgoslin).
• MSnbase: For low-level mass spectrometry data container handling.
• Spectra: For raw mass spectra representation and processing.

Citations

• Liebisch et al. 2020, Journal of Lipid Research (for shorthand nomenclature updates).

References

• Homepage: bioconductor.org/packages/rgoslin
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/rgoslin/inst/doc/introduction.html