qnt.RdIn this TMT 6-plex experiment, four exogenous proteins were spiked into an equimolar Erwinia carotovora lysate with varying proportions in each channel of quantitation; yeast enolase (ENO) at 10:5:2.5:1:2.5:10, bovine serum albumin (BSA) at 1:2.5:5:10:5:1, rabbit glycogen phosphorylase (PHO) at 2:2:2:2:1:1 and bovin cytochrome C (CYT) at 1:1:1:1:1:2. Proteins were then digested, differentially labelled with TMT reagents, fractionated by reverse phase nanoflow UPLC (nanoACQUITY, Waters), and analysed on an LTQ Orbitrap Velos mass spectrometer (Thermo Scientific). Files in multiple format will be used to illustrate the input/output capabilities that are available to the proteomics audience. The companion package provides dedicated functions to directly download the data.
The data has been downloaded from the ProteomeXchange repository and
imported into R as illustrated in the example. It is of class
MSnSet. See also the MSnbase-demo vignette for
more details.
data("qnt")An instance of class MSnSet
Laurent Gatto (2014). RforProteomcs: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publicationR package version 1.3.1.
Gatto L, Christoforou A. Using R and Bioconductor for proteomics data analysis. Biochim Biophys Acta. 2013 May 18. doi:pii: S1570-9639(13)00186-6. 10.1016/j.bbapap.2013.04.032. [Epub ahead of print] PubMed PMID: 23692960.
if (FALSE) {
library("rpx")
px1 <- PXDataset("PXD000001")
mztab <- pxget(px1, "PXD000001_mztab.txt")
library("MSnbase")
qnt <- readMzTabData(mztab, what = "PEP")
sampleNames(qnt) <- reporterNames(TMT6)
qnt$conditions <- factor(c("A", "A", "B", "B", "B", "A"))
qnt <- filterNA(qnt)
selA <- qnt$conditions == "A"
fData(qnt)$log2FC <-
log(rowMeans(exprs(qnt)[, selA]), 2) -
log(rowMeans(exprs(qnt)[, !selA]), 2)
fData(qnt)$baseMean <- log(rowMeans(exprs(qnt)), 10)
}
library("RforProteomics")
library("MSnbase")
data(qnt)
class(qnt)
#> [1] "MSnSet"
#> attr(,"package")
#> [1] "MSnbase"
head(exprs(qnt))
#> TMT6.126 TMT6.127 TMT6.128 TMT6.129 TMT6.130 TMT6.131
#> 2 10630132 11238708 12424917 10997763 9928972 10398534
#> 5 11105690 12403253 13160903 12229367 11061660 10131218
#> 6 1183431 1322371 1599088 1243715 1306602 1159064
#> 8 5384958 5508454 6883086 6136023 5626680 5213771
#> 10 18033537 17926487 21052620 19810368 17381162 17268329
#> 11 9873585 10299931 11142071 10258214 9664315 9518271
head(fData(qnt))
#> sequence accession unit_id unique database database_version
#> 2 DGVSVAR ECA0625 PRIDE_22134 null Erwinia 1
#> 5 NVVLDK ECA0625 PRIDE_22134 null Erwinia 1
#> 6 VEDALHATR ECA0625 PRIDE_22134 null Erwinia 1
#> 8 LAGGVAVIK ECA0625 PRIDE_22134 null Erwinia 1
#> 10 LIAEAMEK ECA0625 PRIDE_22134 null Erwinia 1
#> 11 SFGAPTITK ECA0625 PRIDE_22134 null Erwinia 1
#> search_engine search_engine_score reliability
#> 2 [MS,MS:1001207,Mascot,] [PRIDE,PRIDE:0000069,Mascot score,26.92] null
#> 5 [MS,MS:1001207,Mascot,] [PRIDE,PRIDE:0000069,Mascot score,22.66] null
#> 6 [MS,MS:1001207,Mascot,] [PRIDE,PRIDE:0000069,Mascot score,41.9] null
#> 8 [MS,MS:1001207,Mascot,] [PRIDE,PRIDE:0000069,Mascot score,48.99] null
#> 10 [MS,MS:1001207,Mascot,] [PRIDE,PRIDE:0000069,Mascot score,38.04] null
#> 11 [MS,MS:1001207,Mascot,] [PRIDE,PRIDE:0000069,Mascot score,39.36] null
#> modifications retention_time charge mass_to_charge uri
#> 2 0-MOD:01720 null null null null
#> 5 0-MOD:01720,6-MOD:01720 null null null null
#> 6 0-MOD:01720 null null null null
#> 8 0-MOD:01720,9-MOD:01720 null null null null
#> 10 0-MOD:01720,8-MOD:01720 null null null null
#> 11 0-MOD:01720,9-MOD:01720 null null null null
#> spectra_ref peptide_abundance_stdev_sub[1]
#> 2 ms_file[1]:spectrum=466 null
#> 5 ms_file[1]:spectrum=1604 null
#> 6 ms_file[1]:spectrum=2065 null
#> 8 ms_file[1]:spectrum=2325 null
#> 10 ms_file[1]:spectrum=2712 null
#> 11 ms_file[1]:spectrum=2775 null
#> peptide_abundance_std_error_sub[1] peptide_abundance_stdev_sub[2]
#> 2 null null
#> 5 null null
#> 6 null null
#> 8 null null
#> 10 null null
#> 11 null null
#> peptide_abundance_std_error_sub[2] peptide_abundance_stdev_sub[3]
#> 2 null null
#> 5 null null
#> 6 null null
#> 8 null null
#> 10 null null
#> 11 null null
#> peptide_abundance_std_error_sub[3] peptide_abundance_stdev_sub[4]
#> 2 null null
#> 5 null null
#> 6 null null
#> 8 null null
#> 10 null null
#> 11 null null
#> peptide_abundance_std_error_sub[4] peptide_abundance_stdev_sub[5]
#> 2 null null
#> 5 null null
#> 6 null null
#> 8 null null
#> 10 null null
#> 11 null null
#> peptide_abundance_std_error_sub[5] peptide_abundance_stdev_sub[6]
#> 2 null null
#> 5 null null
#> 6 null null
#> 8 null null
#> 10 null null
#> 11 null null
#> peptide_abundance_std_error_sub[6] log2FC baseMean
#> 2 null -0.04768204 23.38265
#> 5 null -0.11581055 23.47779
#> 6 null -0.17914403 20.31272
#> 8 null -0.21114556 22.46567
#> 10 null -0.12991824 24.14715
#> 11 null -0.06520753 23.27157