gregoire2023_mixCTRL.RdSingle cell proteomics data acquired using the SCoPE2 protocol. The dataset contains two monocytes cell lines (THP1 and U937) as well as controled mixtures of both and macrophage-like cells produced upon PMA treatment. It contains quantitative information at PSM, peptide and protein levels. Data was acquired using Lumos Orbitrap (mainly) and timsTOF SCP mass spectrometers.
gregoire2023_mixCTRLA QFeatures object with 119 assays, each assay being a SingleCellExperiment object:
Assays 1-42: PSM data acquired with a TMT-16plex protocol, hence those assays contain 16 columns. Columns hold quantitative information from single-cell channels, carrier channels, blank (negative control) channels and unused channels.
Assays 43-84: peptide data resulting from the PSM to peptide aggregation of the 42 PSM assays.
Assays 85-91: peptide data for each of the 7 acquisition batches. Peptide data were joined based on their respective acquisition batches.
Assays 92-98: normalised peptide data.
Assays 99-105: normalised and log-transformed peptide data.
Assays 106-112: protein data for each of the 7 acquisition batches. Normalised and log-transformed peptide data were agreggated to protein.
Assays 113-119: Batch corrected protein data. Normalised and log-transformed protein data were batch corrected to remove technical variability induced by runs and channels.
All the data has been filtered to keep high quality features and samples.
The colData(gregoire2023_mixCTRL()) contains cell type annotation and
batch annotation that are common to all assays. The description of
the rowData fields for the PSM data can be found in the
sage documentation.
The data were downloaded from the Zenodo repository. The raw data and
the quantification data can also be found in the ProteomeXchange
Consortium via the PRIDE partner repository,
project PXD046211.
The data were acquired using the following setup. More information can be found in the source article (see References).
Cell isolation: BD FACSAria III cell sorting.
Sample preparation performed using the SCoPE2 protocol: mPOP cell lysis + trypsin digestion + TMT-16plex labeling and pooling.
Separation: online nLC (Ultimate 3000 LC System or Vanquish Neo UHPLC System) with a BioZen Peptide Polar C18 250 x 0.0075mm column.
Mass spectrometry: Orbitrap Fusion Lumos Tribrid (MS1 resolution = 70,000; MS2 accumulation time = 120ms; MS2 resolution = 70,000) and timsTOF SCP.
Data preprocessing: Sage.
The PSM data were collected from a Zenodo archive (see Source
section). The folder contains the following files of interest:
results.sage.cbio.tsv: the sage identification output file for
batches acquired on the Lumos MS.
results.sage.giga.tsv: the sage identification output file for
batches acquired on the timsTOF SCP MS.
quant.cbio.tsv: the sage quantification output file for
batches acquired on the Lumos MS.
quant.giga.tsv: the sage quantification output file for
batches acquired on the timsTOF SCP MS.
sampleAnnotation_batch.csv: sample annotation for each
acquisition batch. There are in total 8 different annotation
files.
We combined the sample annotations in a single table. We also
combined cbio and giga tables together and merged resulting
identification and quantification tables. Both annotation and
features tables are then combined in a single QFeatures object
using the scp::readSCP() function.
The QFeatures object was processed as described in the author's
manuscript (see source). Note that the imputed assays were used
in the paper for illustrative purposes only and have not been
reproduced here.
Samuel Grégoire, Christophe Vanderaa, Sébastien Pyr dit Ruys, Gabriel Mazzucchelli, Christopher Kune, Didier Vertommen and Laurent Gatto. 2023. Standardised workflow for mass spectrometry- based single-cell proteomics data processing and analysis using the scp package. arXiv. DOI:10.48550/arXiv.2310.13598
# \donttest{
gregoire2023_mixCTRL()
#> see ?scpdata and browseVignettes('scpdata') for documentation
#> loading from cache
#> An instance of class QFeatures containing 119 assays:
#> [1] CBIO680_1: SingleCellExperiment with 1862 rows and 3 columns
#> [2] CBIO680_3: SingleCellExperiment with 1941 rows and 1 columns
#> [3] CBIO680_4: SingleCellExperiment with 1948 rows and 3 columns
#> ...
#> [117] proteins_CBIO725_batchC: SingleCellExperiment with 1360 rows and 70 columns
#> [118] proteins_CBIO754_batchC: SingleCellExperiment with 1801 rows and 33 columns
#> [119] proteins_GIGA_batchC: SingleCellExperiment with 1629 rows and 26 columns
# }