Paired lung nodule glycoproteomics

Usage

glyhub_PXD046637_N_Lung(
  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/s41467-025-57364-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

39,079 source feature rows across 165 reported measurement columns.

Assay scale: Deposited untransformed ion-level TMT reporter intensities; author software aggregated PSMs to ions

Feature grain: Peptide Sequence / Modified Sequence / Charge / Observed Modifications / Protein

Source selection: Raw deposited ion reporter table preferred. Processed clinical matrix retained as explicit alternative in metadata because original channel-to-patient mapping was not supplied in the inspected files.

No additional normalization, logarithm, imputation, zero conversion, confidence filtering or intensity aggregation

Exact molecular identity union across batches; an ion absent from a batch becomes structural NA

All source ion rows, including rows without glycan annotations, and all 11 channels per batch retained

165 reporter channels are not 165 patients: reference/unused roles and linkage to the 132 clinical specimens remain unresolved

Source annotation.txt only repeats channel labels; clinical specimen labels are not guessed

Source PSM-to-ion summarization precedes this deposit; upstream correction settings remain unverified

Unambiguous composition text parsed after removing its explicit terminal mass; ambiguous modifications retain full text and typed NA

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.

Availability and source license

Downloaded from the existing data release through the verified cache. Source-license scope for the complete object remains unresolved; no new license is granted. See publication-decisions.tsv and object metadata for original sources and limitations.