LOPIT data from Tan et al. 2009

Description

This is the data from Tan et al., Mapping organelle proteins and protein complexes in Drosophila melanogaster, J Proteome Res. 2009 Jun;8(6):2667-78. See below for more details.

Usage

data(tan2009r1)
data(tan2009r2)
data(tan2009r3)
data(tan2009r1goCC)

Format

The data is an instance of class MSnSet from package MSnbase.

Details

This is a LOPIT experiment. Normalised intensities for proteins for four iTRAQ 4-plex labelled fractions are available for 3 replicates (r1, r2 and r3 respectively). The partial least square discriminant analysis results from the paper are available as PLSDA feature meta-data and the markers used in analysis are available as markers feature meta-data (Note: the ER and Golgi organelle markers were combined in original PLSDA analysis).

Replicate 1 was also used in testing the phenotype discovery algorithm from Breckels et al., The Effect of Organelle Discovery upon Sub-Cellular Protein Localisation, J Proteomics, In Press., see phenoDisco. New phenotype clusters identified from algorithm application are available as pd.2013 feature meta-data.

The tan2009r1goCC instance contains binary assay data. Its columns represent GO CC terms that have been observed for the object's features. A 1 indicates that a GO term has been associated to a given feature (protein); a 0 means not such association was found in the GO ontology.

Source

Supporting Information on http://pubs.acs.org/doi/full/10.1021/pr800866n

References

Mapping organelle proteins and protein complexes in Drosophila melanogaster. Tan DJ, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS. J Proteome Res. 2009 Jun;8(6):2667-78. PMID: 19317464

Breckels LM, Gatto L, Christoforou A, Groen AJ, Lilley KS and Trotter MWB. The Effect of Organelle Discovery upon Sub-Cellular Protein Localisation J Proteomics. In Press.

Examples

data(tan2009r1)
tan2009r1
pData(tan2009r1)
head(exprs(tan2009r1))
# Organelle markers
table(fData(tan2009r1)$markers)
# PLSDA assignment results
table(fData(tan2009r1)$PLSDA)

Results

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> library(pRolocdata)
Loading required package: MSnbase
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is pRolocdata version 1.10.0.
Use 'pRolocdata()' to list available data sets.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pRolocdata/tan2009.Rd_%03d_medium.png", width=480, height=480)
> ### Name: tan2009
> ### Title: LOPIT data from Tan et al. 2009
> ### Aliases: tan2009 tan2009r1 tan2009r2 tan2009r3 tan2009r1goCC
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(tan2009r1)
> tan2009r1
MSnSet (storageMode: lockedEnvironment)
assayData: 888 features, 4 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: X114 X115 X116 X117
  varLabels: Fractions
  varMetadata: labelDescription
featureData
  featureNames: P20353 P53501 ... P07909 (888 total)
  fvarLabels: FBgn Protein.ID ... markers.tl (16 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 19317464 
Annotation:  
- - - Processing information - - -
Added markers from  'mrk' marker vector. Thu Jul 16 22:53:44 2015 
 MSnbase version: 1.17.12 
> pData(tan2009r1)
     Fractions
X114       4/5
X115     12/13
X116        19
X117        21
> head(exprs(tan2009r1))
           X114     X115     X116     X117
P20353 0.379000 0.281000 0.225000 0.114000
P53501 0.420000 0.209667 0.206111 0.163889
Q7KU78 0.187333 0.167333 0.169667 0.476000
P04412 0.247500 0.253000 0.320000 0.179000
Q7KJ73 0.216000 0.183000 0.342000 0.259000
Q7JZN0 0.072000 0.212333 0.573000 0.142667
> # Organelle markers
> table(fData(tan2009r1)$markers)

 Cytoskeleton            ER         Golgi      Lysosome       Nucleus 
            7            28            13             8            21 
           PM    Peroxisome    Proteasome  Ribosome 40S  Ribosome 60S 
           34             4            15            20            32 
mitochondrion       unknown 
           29           677 
> # PLSDA assignment results
> table(fData(tan2009r1)$PLSDA)

     ER/Golgi mitochondrion            PM       unknown 
          235            74           180           399 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>