R/liang2020_hela.R

In UCLouvain-CBIO/scpdata: Single-Cell Proteomics Data Package

##' Liang et al. 2020 (Anal. Chem.): HeLa cells (MaxQuant preprocessing)
##'
##' Single-cell proteomics data from HeLa cells using the autoPOTS
##' acquisition workflow. The samples contain either no cells (blanks),
##' 1 cell, 10 cells, 150 cells or 500 cells. Samples containing
##' between 0 and 10 cells are isolated using micro-pipetting while
##' samples containing between 150 and 500 cells were prepared using
##' dilution of a bulk sample.
##'
##' @format A [QFeatures] object with 17 assays, each assay being a
##' [SingleCellExperiment] object:
##'
##' - `HeLa_*`: 15 assays containing PSM data.
##' - `peptides`: quantitative data for 48705 peptides in 15 samples
##'   (all runs are combined).
##' - `proteins`: quantitative data for 3970 protein groups in 15
##'   samples (all runs combined).
##'
##' Sample annotation is stored in `colData(liang2020_hela())`.
##'
##' @section Acquisition protocol:
##'
##' The data were acquired using the following setup. More information
##' can be found in the source article (see `References`).
##'
##' - **Cell isolation**: The HeLa cells come from a commercially
##'   available cell line. Samples containing between 0 and 10 cells
##'   were isolated using micro-manipulation and the counts were
##'   validated using a microscope. Samples containing between 150 and
##'   500 cells were prepared by diluting a bulk sample and the exact
##'   counts were evaluated by obtaining phtotmicrographs.
##' - **Sample preparation** performed using the autoPOTS worflow that
##'   relied on the OT-2 pipeting robot. Cell are lysed using
##'   sonication. Samples are then processed by successive incubation
##'   with DTT (reduction), then IAA (alkylation), then Lys-C and
##'   trypsin (protein digestion).
##' - **Separation**: Samples were injected on the column using a
##'   modified Ultimate WPS-3000 TPL autosampler coupled to an UltiMate
##'   3000 RSLCnano pump. The LC column is a home-packed nanoLC column
##'   (45cm x 30um; 40nL/min)
##' - **Ionization**: Nanospray Flex ion source (2,000V)
##' - **Mass spectrometry**: Orbitrap Exploris 480. MS1 settings:
##'   accumulation time = 250 ms (0-10 cells) or 100 ms (150-500 cells);
##'   resolution = 120,000; AGC = 100\%. MS2 settings: exlusion
##'   duration = 90 s (0-10 cells) or 60 s (150-500 cells) ; accumulation
##'   time = 500 ms (0-1 cell), 250 ms (10 cells), 100 ms (150 cells)
##'   or 50 ms (500 cells); resolution = 60,000 (0-10 cells) or 30,000
##'   (150-500 cells); AGC = 5E3 (0-1 cells) or 1E4 (10-500 cells).
##' - **Data analysis**: MaxQuant (v1.6.7.0) and the search database
##'   is Swiss-Prot (July 2020).
##'
##' @section Data collection:
##'
##' All data were collected from the PRIDE repository (accession ID:
##' PXD021882).
##'
##' The sample annotations were collected from the methods section and
##' from table S3 in the paper.
##'
##' The PSM data were found in the `evidence.txt` file. The data were
##' converted to a [QFeatures] object using the [scp::readSCP()]
##' function.
##'
##' The peptide data were found in the `peptides.txt` file. The column
##' names holding the quantitative data were adapted to match the
##' sample names in the [QFeatures] object. The data were then
##' converted to a [SingleCellExperiment] object and then inserted in
##' the [QFeatures] object. Links between the PSMs and the peptides
##' were added
##'
##' A similar procedure was applied to the protein data. The data were
##' found in the `proteinGroups.txt` file. The column names were
##' adapted, the data were converted to a [SingleCellExperiment]
##' object and then inserted in the [QFeatures] object. Links between
##' the peptides and the proteins were added
##'
##' @source
##' The PSM data can be downloaded from the PRIDE repository
##' PXD021882 The source link is:
##' http://ftp.pride.ebi.ac.uk/pride/data/archive/2020/12/PXD021882/
##'
##' @references
##'
##' Liang, Yiran, Hayden Acor, Michaela A. McCown, Andikan J. Nwosu,
##' Hannah Boekweg, Nathaniel B. Axtell, Thy Truong, Yongzheng Cong,
##' Samuel H. Payne, and Ryan T. Kelly. 2020. “Fully Automated Sample
##' Processing and Analysis Workflow for Low-Input Proteome
##' Profiling.” Analytical Chemistry, December.
##' ([link to article](https://doi.org/10.1021/acs.analchem.0c04240)).
##'
##' @examples
##' \donttest{
##' liang2020_hela()
##' }
##'
##' @keywords datasets
##'
"liang2020_hela"