brunner2022: Brunner et al. 2022 (Mol. Syst. Biol.): cell cycle state...

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

Brunner et al. 2022 (Mol. Syst. Biol.): cell cycle state study

Description

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.

Usage

brunner2022

Format

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.

Acquisition protocol

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).

Data collection

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.

Source

The data were downloaded from PRIDE repository with accession ID PXD024043.

References

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

Examples

brunner2022()

UCLouvain-CBIO/scpdata documentation built on Oct. 29, 2024, 4:22 p.m.