O-glycan profile of Fetuin_standard and related study experiments

Complete O-glycan peak-area profile from source panel S2 Fetuin_standard, in the study of cell-line-specific O-glycosylation. All 3 source quantitative features and 3 replicate observations are retained. Combined O-glycan quantitative profiles from GPST000035. 231 union features and 66 source observations are represented.

Usage

glyhub_GPST000035_O(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Format

A glyexp::GlycomicSE with 231 features and 66 observations. The abundance assay is in peak_area. rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000035. S2 Fetuin_standard. Study: https://doi.org/10.1007/s00018-020-03504-z. Repository: https://glycopost.glycosmos.org/entry/GPST000035. Quantitative source: https://media.springernature.com/original/springer-static/esm/art%3A10.1007%2Fs00018-020-03504-z/MediaObjects/18_2020_3504_MOESM4_ESM.xlsx.

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.

Details

Source experiments are identified in colData and original panel-specific metadata, annotations and measurements are retained in metadata. Feature identities are aligned only when supported by author identifiers or explicit molecular structures; other features retain source-specific identities. The source_coverage matrix distinguishes unmeasured combinations from measured missing values. Units: peak_area.

O-glycan profile of Fetuin_standard: The 3 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of C10: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of COLO205 : The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of HT29: The 3 observations are source-labelled biological replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of HT29_Vumc : The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of WiDr: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of KM12: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of T84 : The 2 observations are source-labelled unspecified replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of LS174T: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of LS180: The 2 observations are source-labelled unspecified replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of SW1116: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of SW1463: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of SW948: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of SW1398: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of SW48: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of SW480: The 3 observations are source-labelled biological replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of SW480_Vumc : The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of SW620: The 3 observations are source-labelled biological replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of SW837: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of CaCo-2: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of Co115 : The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of Colo320: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of DLD-1: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of HCT116: The 3 observations are source-labelled biological replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of HCT116 Vumc: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of HCT 15: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of HCT 8 : The 3 observations are source-labelled biological replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of LOVO: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of LS411N: The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

O-glycan profile of RKO : The 2 observations are source-labelled technical replicates in this panel. Source biological and technical replicate designations are retained in colData where stated. Source retention-time isomers retain distinct feature identities unless the author global identifier, composition, retention time and relative area establish a match. Fetuin is a quality-control standard rather than a cell line. Source monosaccharide-count conflicts produce unknown typed composition, while the original label, counts and quantitative matrix are preserved. Sulfation is encoded as a substituent where supported.

Molecular annotations retain source precision. Unresolved compositions or structures are NA; original annotations are retained in rowData. All quantitative source features are preserved.

Access

Use glyhub_load("glyhub_GPST000035_O") to load this dataset.