brunner2022.RdSingle cell proteomics data acquired by the Mann Lab using a newly designed timsTOF instrument, referred to as timsTOF-SCP. The dataset contains quantitative information from single-cells blocked at 4 cell cycle stages: G1, G1-S, G2, G2-M. The data was acquired using a label-free sample preparation protocole combined to a data independent (DIA) acquisition mode.
brunner2022A QFeatures object with 435 assays, each assay being a SingleCellExperiment object.
Assay 1-434: DIA-NN main output report table split for each acquisition run. Since each run acquires 1 single cell, each assay contains a single column. It contains the results of the spectrum identification and quantification.
protein: DIA-NN protein group matrix, containing normalised
quantities for 2476 protein groups in 434 single cells. Proteins
are filtered at 1% FDR, using global q-values for protein groups
and both global and run-specific q-values for precursors.
The colData(brunner2022()) contains cell type annotations and
batch annotations. The description of the rowData fields for the
different assays can be found in the
DIA-NN documentation.
The data were downloaded from PRIDE
repository
with accession ID PXD024043.
The data were acquired using the following setup. More information
can be found in the source article (see References).
Cell isolation: cells were detached with trypsin treatment, followed by strong pipetting, and isolate using FACS.
Sample preparation: cell lysis by freeze-heat followed by sonication, overnight protein digestion with trypsin/lysC mix and desalting using EvoTips trap column (EvoSep)
Separation: online EvoSep One LC system using a 5 cm x 75 µm ID column with 1.9µm C18 beads (EvoSep) at 100nL/min flow rate.
Ionization: 10µm ID zero dead volume electrospray emitter (Bruker Daltonik) + nanoelectro-spray ion source (Captive spray, Bruker Daltonik)
Mass spectrometry: DIA PASEF mode. Correlation between IM and m/z was used to synchronize the elution of precursors from each IM scan with the quadrupole isolation window. Five consecutive diaPASEF cycles. The collision energy was ramped linearly as a function of the IM from 59 eV at 1/K0=1.6 Vs cm^2 to 20 eV at 1/K0=0.6 Vs cm^2.
Data analysis: DIA-NN (1.8).
The data were collected from the PRIDE
repository
in the DIANN1.8_SingleCells_CellCycle.zip file.
We loaded the DIA-NN main report table and generated a sample
annotation table based on the MS file names. We next combined the
sample annotation and the DIANN tables into a QFeatures object
following the scp data structure. We loaded the proteins group
matrix as a SingleCellExperiment object, fixed ambiguous
protein group names, and added the protein data as a new assay and
link the precursors to proteins using the Protein.Group variable
from the rowData.
Brunner, Andreas-David, Marvin Thielert, Catherine Vasilopoulou, Constantin Ammar, Fabian Coscia, Andreas Mund, Ole B. Hoerning, et al. 2022. "Ultra-High Sensitivity Mass Spectrometry Quantifies Single-Cell Proteome Changes upon Perturbation." Molecular Systems Biology 18 (3): e10798. Link to article
# \donttest{
brunner2022()
#> see ?scpdata and browseVignettes('scpdata') for documentation
#> loading from cache
#> An instance of class QFeatures containing 435 assays:
#> [1] D:\Andreas_Brunner\Projects\SingleCellProteomics\202109_WorkHere\SingleCells\SingleShots_RawData\20201009_TIMS04_Evo07_AnBr_1Cell_HeLa_NB_01_S3-G2_1_3873.d: SingleCellExperiment with 3772 rows and 1 columns
#> [2] D:\Andreas_Brunner\Projects\SingleCellProteomics\202109_WorkHere\SingleCells\SingleShots_RawData\20201009_TIMS04_Evo07_AnBr_1Cell_HeLa_NB_02_S3-G3_1_3874.d: SingleCellExperiment with 7759 rows and 1 columns
#> [3] D:\Andreas_Brunner\Projects\SingleCellProteomics\202109_WorkHere\SingleCells\SingleShots_RawData\20201009_TIMS04_Evo07_AnBr_1Cell_HeLa_NB_03_S3-G4_1_3875.d: SingleCellExperiment with 4481 rows and 1 columns
#> ...
#> [433] D:\Andreas_Brunner\Projects\SingleCellProteomics\202109_WorkHere\SingleCells\SingleShots_RawData\20201126_TIMS04_Evo07_SA_ADB_1cell_HeLa_UB_98_S2-C2_1_5109.d: SingleCellExperiment with 2569 rows and 1 columns
#> [434] D:\Andreas_Brunner\Projects\SingleCellProteomics\202109_WorkHere\SingleCells\SingleShots_RawData\20201126_TIMS04_Evo07_SA_ADB_1cell_HeLa_UB_99_S2-C3_1_5110.d: SingleCellExperiment with 2327 rows and 1 columns
#> [435] proteins: SingleCellExperiment with 2476 rows and 434 columns
# }