data: Example data for 100 proteins

In statOmics/msqrob2: Robust statistical inference for quantitative LC-MS proteomics

Example data for 100 proteins

Description

Subset of peptides from 100 proteins from a quantitative mass spectrometry based proteomics dataset (PRIDE identifier: PXD003881 Shen et al. (2018)). E. Coli lysates were spiked at five different concentrations (3%, 4.5%, 6%, 7.5% and 9%wt/wt) in a stable human background (4 repl. per treatment). The twenty resulting samples were run on an Orbitrap Fusion mass spectrometer. Raw data files were processed with MaxQuant (version 1.6.1.0, Cox and Mann (2008)) using default search settings unless otherwise noted. Spectra were searched against the UniProtKB/SwissProt human and E. Coli reference proteome databases (07/06/2018), concatenated with the default Maxquant contaminant database. Carbamidomethylation of Cystein was set as a fixed modification, and oxidation of Methionine and acetylation of the protein amino-terminus were allowed as variable modifications. In silico cleavage was set to use trypsin/P, allowing two miscleavages. Match between runs was also enabled using default settings. The resulting peptide-to-spectrum matches (PSMs) were filtered by MaxQuant at 1% FDR.

Usage

data(pe)

Format

Feature set with an instance "peptide":

assay

contains the raw peptide intensities

rowData

contains a variable "Proteins" with the protein accession and an variable ecoli to indicate if the protein is a spikin.

colData

contains a factor condition indicating the spike-in condition

Examples

data(pe)
head(colData(pe))
head(rowData(pe))
head(assay(pe))

statOmics/msqrob2 documentation built on May 8, 2024, 4:38 p.m.