brunner2022 | R Documentation |
Single 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.
brunner2022
A 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 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
.
The data were downloaded from PRIDE
repository
with accession ID PXD024043
.
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
brunner2022()
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