qnt: PXD000001 example MSnSet

In lgatto/RforProteomics: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication

PXD000001 example MSnSet

Description

In 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.

Usage

data("qnt")

Format

An instance of class MSnSet

References

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.

Examples

## Not run: 
    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)

## End(Not run)

library("RforProteomics")
library("MSnbase")
data(qnt)
class(qnt)
head(exprs(qnt))
head(fData(qnt))

lgatto/RforProteomics documentation built on May 10, 2023, 11:51 p.m.