% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/wu2026.R
\docType{data}
\name{wu2026}
\alias{wu2026}
\title{Wu et al., 2026 (Nature Biotechnology): single-cell proteomic landscape
of the developing human brain}
\format{
A \link[QFeatures:QFeatures-class]{QFeatures::QFeatures} object with 2313 sets, each set being a
\link[SingleCellExperiment:SingleCellExperiment]{SingleCellExperiment::SingleCellExperiment} object:
\itemize{
\item Set 1-2310: log-transformed precursor-level single-cell data (one
column per set) from DIA-NN reports.
\item \code{peptides}: peptide-level data containing quantitative data for 17755
peptides in 2310 single cells.
\item \code{imported_proteins}: protein-level table imported from the authors'
protein report, containing 4401 proteins in 2310 single cells.
\item \code{proteins}: protein-level data containing quantitative data for 5107
proteins in 2310 single cells.
}

Sample annotation is stored in \code{colData(wu2026())}.
}
\source{
The data were downloaded from the PRIDE repository with accession ID
\code{PXD071075}:
https://www.ebi.ac.uk/pride/archive/projects/PXD071075
}
\usage{
wu2026
}
\description{
Label-free single-cell proteomics data from prenatal human brain tissue
(gestational weeks 13, 15 and 19), generated to characterize cell-type
proteomes and developmental trajectories at single-cell resolution.
}
\section{Acquisition protocol}{


The data were acquired using the following setup. More information
can be found in the source article (see \code{References}).
\itemize{
\item \strong{Sample isolation}: fresh prenatal human brain tissue was dissociated
and single cells were sorted by FACS (Sony SH800) into 384-well low-bind
plates.
\item \strong{Sample preparation}: cells were lysed in low-volume TEAB-based buffer,
digested overnight with trypsin, acidified with trifluoroacetic acid,
and desalted on EvoTip Pure.
\item \strong{Liquid chromatography}: peptides were separated on an IonOpticks Aurora
Elite XT C18 nano-LC column (15 cm x 75 micrometer) on an Evosep One
using a 31-minute gradient.
\item \strong{Mass spectrometry}: Orbitrap Eclipse Tribrid with FAIMS Pro was used
in DIA mode.
\item \strong{Raw data processing}: DIA-NN against the UniProt human reference
proteome.
}
}

\section{Data collection}{


The \code{QFeatures} object was built from the DIA-NN peptide and protein report
tables and a sample annotation table. PSM-level data were imported with
\code{\link[scp:readSCP]{scp::readSCP()}}, log-transformed, aggregated to peptide-level features, and
joined across single-cell runs. The protein report table was imported as a
\link[SingleCellExperiment:SingleCellExperiment]{SingleCellExperiment::SingleCellExperiment}, added as an set, and linked to peptide-level data.

The script to reproduce the \code{QFeatures} object is available at
\code{inst/scripts/make-data_wu2026.R}.
}

\examples{
\donttest{
wu2026()
}

}
\references{
Wu, T., Jiang, L., Mukhtar, T., Wang, L., Jian, R., Wang, C., Trinh, T.,
Kriegstein, A. R., Snyder, M., and Li, J. 2026. "Single-cell proteomic
landscape of the developing human brain." Nature Biotechnology.
\href{https://doi.org/10.1038/s41587-025-02980-7}{Link to article}
}
\keyword{datasets}
