isobar-data: Isobar Data packages

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

ibspiked_set1 and ibspiked_set2 are objects of class iTRAQ4plexSpectra. It contains over 160 protein groups, over 1600 peptides from about 15,000 spectra each, mainly from background proteins and three spiked-in Ceruplasmins (CERU_HUMAN, CERU_MOUSE, CERU_RAT).

Usage

  data(ibspiked_set1)
  data(ibspiked_set2)
  data(ib_phospho)

Format

iTRAQ4plexSpectra objects.

Source

isobar publication. Acquired on Orbitrap instrument w/ 20 offline-fractions and HCD fragmentation.

Examples

data(ibspiked_set1)
print(ibspiked_set1)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to isobar (v 1.22.0)
   'openVignette("isobar")' and '?isobar' provide help on usage.


Attaching package: 'isobar'

The following object is masked from 'package:BiocGenerics':

    normalize

The following object is masked from 'package:base':

    paste0

iTRAQ4plexSpectra (storageMode: lockedEnvironment)
assayData: 14991 features, 4 samples 
  element names: ions, mass 
protocolData: none
phenoData: none
featureData
  featureNames: M261-D07-HS-P1948-1.1765.1765.2.dta.38373
    M261-C07-HS-P1948-1.2376.2376.3.dta.26320 ...
    M261-D06-HS-P1948-1.1660.1660.3.dta.37304 (14991 total)
  fvarLabels: peptide modif ... use.for.quant (12 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
14991  spectra
ProteinGroup object
    1653 peptides are detected
     157 protein groups with specific peptides

isobar documentation built on Nov. 8, 2020, 7:48 p.m.