R/pxd014777.R

In msImpute: Imputation of label-free mass spectrometry peptides

#' Processed peptide intensity matrix from PXD014777 study
#'
#' A Trapped Ion Mobility Spectrometry (TIMS) dataset of blood plasma from a number of patients acquired in two batches.
#' This is a technical dataset
#' published by MaxQuant to benchmark their software for ion mobility enhanced shotgun proteomics.
#' Rows are Modified Peptide IDs. Charge state variations are treated as distinct peptide species.
#' For peptides with multiple identification types, the intensity is considered to be the median of reported intensity values.
#' Reverse complememts and contaminant peptides are discarded.
#' Peptides with more than 4 observed intensity values are retained.
#' This object contains data from peptide.txt table output by MaxQuant.
#' The evidence.txt file can be downloaded as RDS object from \url{https://github.com/soroorh/proteomicscasestudies}.
#' Code for data processing is provided in package vignette.
#'
#' @format A matrix
#' @references
#' Prianichnikov N, Koch H, Koch S, Lubeck M, Heilig R, Brehmer S, Fischer R, Cox J, MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics. Mol Cell Proteomics, 19(6):1058-1069(2020)
#' @source \url{http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD014777}
"pxd014777"