DQGlyco microbiome experiment reporter intensities

Usage

glyhub_PXD052447_N_Microbiome(
  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/s41594-025-01485-w.

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

160,699 source feature rows across 18 reported measurement columns.

Assay scale: Deposited untransformed PSM-level TMT reporter intensities

Feature grain: PSM; all deposited rows retained, including rows without glycan annotation

Source selection: Deposited reporter intensities preferred over normalized supplementary glycopeptide matrices or ratios

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

Source blanks are NA; numeric zero retained with no interpretation of its missingness semantics

All 18 deposited reporter channels retained; unmatched channel roles remain unknown

PSM counts are not counts of unique glycopeptides; no peptide-level aggregation performed

Protein sites are not inferred from peptide coordinates; original search annotations are retained

Source search/FDR and reporter extraction precede this deposit; any undocumented upstream correction remains unknown

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.

All deposited PSM rows are retained, including rows without a glycan annotation. All source reporter channels are retained; unmapped channels have unknown sample roles. Consult sample_annotation_matched before comparing biological groups.

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.