Glyco-DIA precursor peak areas in a dilution experiment

Usage

glyhub_PXD011063_O_Dilution(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Source

https://doi.org/10.1038/s41592-019-0504-x.

Arguments

kind: "curated" returns a data object; "raw" returns the path to a verified source archive. Raw archives are currently available for CPTAC.
cache_dir: Cache directory, defaulting to tools::R_user_dir("glyhub", "cache"). Set option glyhub.cache_dir to change the default.
refresh: Download the pinned resource again, even if cached.
offline: Prohibit downloads; require a verified local resource.

Value

A glyexp::GlycoproteomicSE.

Details

15,890 source feature rows across 10 reported measurement columns.

Assay scale: Source FG.MS2TotalPeakArea; untransformed summed MS2 fragment chromatographic peak area

Feature grain: Library-specific precursor and source decoy flag; source decoys retained and explicitly flagged

Source selection: MS2TotalPeakArea preferred over FG.Quantity, EG.TotalQuantity and supplementary glycopeptide quantities; MS1PeakArea retained in metadata

No normalization, log transform, imputation, zero conversion, confidence filtering or aggregation

Union of exact library/precursor/decoy keys; absent report rows become structural NA, not zero

Source decoy rows and unquantified or unidentified rows retained; use source flags before biological inference

Different libraries are alternative analyses, not independent biological samples

No glycan composition inferred solely from rounded modification mass; source modified sequence retained

Spectronaut extraction, interference handling and upstream settings are not fully recoverable from these exports

Measurement columns are not automatically independent biological samples. Source row identifiers, annotations and provenance are retained in metadata.

The assay preserves source numeric values. The metadata field raw_abundance means source numbers; it does not certify that the authors supplied unprocessed intensity.

Source decoys are retained and flagged; this is an unfiltered source-report representation, not a confidence-filtered biological feature set.

Availability and source license

Downloaded from the existing data release through the verified cache. Deposited PRIDE source data are CC0-1.0, explicitly declared in the project API. Cite the original authors and accession; see metadata redistribution and source provenance.