scpdata: Single-Cell Proteomics Data Package

##' Zhu et al. 2018 (Mol. Cel. Prot.): rat brain laser dissections
##'
##' Near single-cell proteomics data of laser captured
##' micro-dissection samples. The samples are 24 brain sections from
##' rat pups (day 17). The slices are 12 um thick squares of either
##' 50, 100, or 200 um width. 5 samples were dissected from the corpus
##' callum (`CC`), 4 samples were dissected from the corpus collosum
##' (`CP`), 13 samples were extracted from the cerebral cortex
##' (`CTX`), and 2 samples are labeled as (`Mix`).
##'
##' @format A [QFeatures] object with 4 assays, each assay being a
##' [SingleCellExperiment] object:
##'
##' - `peptides`: quantitative information for 13,055 peptides from
##'   24 samples
##' - `proteins_intensity`: protein intensities for 2,257 proteins
##'   from 24 samples
##' - `proteins_LFQ`: LFQ intensities for 2,257 proteins from 24 samples
##' - `proteins_iBAQ`: iBAQ values for 2,257 proteins from 24 samples
##'
##' Sample annotation is stored in `colData(zhu2018MCP())`.
##'
##' @section Acquisition protocol:
##'
##' The data were acquired using the following setup. More information
##' can be found in the original article (see `References`).
##'
##' - **Cell isolation**: brain patches were collected using
##'   laser-capture microdissection (PALM MicroBeam) on flash frozen
##'   rat (*Rattus norvergicus*) brain tissues. Note that the samples
##'   were stained with H&E before dissection for histological
##'   analysis. DMSO is used as sample collection solution
##' - **Sample preparation** performed using the nanoPOTs device: DMSO
##'   evaporation + protein extraction (DMM + DTT) + alkylation (IAA)
##'   + Lys-C digestion + trypsin digestion.
##' - **Separation**: nanoLC (Dionex UltiMate with an in-house packed
##'   60cm x 30um LC columns; 50nL/min)
##' - **Ionization**: ESI (2,000V)
##' - **Mass spectrometry**: Thermo Fisher Orbitrap Fusion Lumos
##'   Tribrid (MS1 accumulation time = 246ms; MS1 resolution =
##'   120,000; MS1 AGC = 3E6). The MS/MS settings  depend on the
##'   sample size, excepted for the AGC = 1E5. 50um (time = 502ms;
##'   resolution = 240,000), 100um (time = 246ms; resolution =
##'   120,000), 200um (time = 118ms; resolution = 60,000).
##' - **Data analysis**: MaxQuant (v1.5.3.30) + Perseus (v1.5.6.0) +
##'   Origin Pro 2017
##'
##' @section Data collection:
##'
##' The data were collected from the PRIDE repository (accession
##' ID: PXD008844).  We downloaded the `MaxQuant_Peptides.txt`
##' and the `MaxQuant_ProteinGroups.txt` files containing the
##' combined identification and quantification
##' results. The sample annotations were inferred from the names of
##' columns holding the quantification data and the information in the
##' article. The peptides data were converted to a [SingleCellExperiment]
##' object. We split the protein table to separate the three types of
##' quantification: protein intensity, label-free quantitification
##' (LFQ) and intensity based absolute quantification (iBAQ). Each
##' table is converted to a [SingleCellExperiment] object along with
##' the remaining protein annotations. The 4 objects are combined in
##' a single [QFeatures] object and feature links are created based on
##' the peptide leading razor protein ID and the protein ID.
##'
##' @source
##' The PSM data can be downloaded from the PRIDE repository
##' PXD008844. FTP link
##' ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/07/PXD008844
##'
##' @references
##' Zhu, Ying, Maowei Dou, Paul D. Piehowski, Yiran Liang, Fangjun
##' Wang, Rosalie K. Chu, William B. Chrisler, et al. 2018. “Spatially
##' Resolved Proteome Mapping of Laser Capture Microdissected Tissue
##' with Automated Sample Transfer to Nanodroplets.” Molecular &
##' Cellular Proteomics: MCP 17 (9): 1864–74
##' ([link to article](http://dx.doi.org/10.1074/mcp.TIR118.000686)).
##'
##' @examples
##' \donttest{
##' zhu2018MCP()
##' }
##'
##' @keywords datasets
##'
##'
"zhu2018MCP"