Glyco-DIA SA serum source precursor peak areas

Usage

glyhub_PXD011063_O_SerumSA(
  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

93,442 source feature rows across 6 reported measurement columns.

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

Feature grain: Library / precursor / decoy flag; all source row associations retained

Source selection: Original Spectronaut peak areas preferred over author-added Abundance and derived summary statistics

No normalization, logarithm, imputation, zero conversion, confidence filtering or numerical aggregation

Repeated DDA-association rows are represented by their shared quantitative cell only after exact MS1/MS2 equality is proven; no value averaging or conflict resolution

Every source association remains linked by file and row; a missing precursor/run pair becomes structural NA

Source decoy rows retained and flagged; biological independence of runs is not inferred from filenames

Source modified sequence and glycopeptide label retained; no glycan composition inferred solely from rounded mass

Upstream extraction and interference handling are not fully documented in 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.

Only the SA source file is included, across six reported runs. The deSA source CSV contains independently confirmed embedded NUL bytes and an unparsable quantitative record; it is excluded, not repaired or filtered. All source decoys are retained and flagged. Biological independence and exact glycan compositions remain unassigned.

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.