petrosius2023_mES: Petrosius et al, 2023 (Nat. Comm.): Mouse embryonic stem cell...
In UCLouvain-CBIO/scpdata: Single-Cell Proteomics Data Package

petrosius2023_mES

R Documentation

Petrosius et al, 2023 (Nat. Comm.): Mouse embryonic stem cell (mESC) in different culture conditions

Description

Profiling mouse embryonic stem cells across ground-state (m2i) and differentiation-permissive (m15) culture conditions. The data were acquired using orbitrap-based data-independent acquisition (DIA). The objective was to demonstrate the capability of their approach by profiling mouse embryonic stem cell culture conditions, showcasing heterogeneity in global proteomes, and highlighting differences in the expression of key metabolic enzymes in distinct cell subclusters.

Usage

petrosius2023_mES

Format

A QFeatures object with 605 assays, each assay being a SingleCellExperiment object:

Assay 1-603: PSM data acquired with an orbitrap-based data-independent acquisition (DIA) protocol, hence those assays contain single column that contains the quantitative information.
peptides: peptide data containing quantitative data for 9884 peptides and 603 single-cells.
proteins: protein data containing quantitative data for 4270 proteins and 603 single-cells.

Sample annotation is stored in colData(petrosius2023_mES()).

Acquisition protocol

The data were acquired using the following setup. More information can be found in the source article (see References).

Sample isolation: Cell sorting was done on a Sony MA900 cell sorter using a 130 microm sorting chip. Cells were sorted at single-cell resolution, into a 384-well Eppendorf LoBind PCR plate (Eppendorf AG) containing 1 microL of lysis buffer.
Sample preparation: Single-cell protein lysates were digested with 2 ng of Trypsin supplied in 1 microL of digestion buffer which was carried out overnight at 37 °C, and subsequently acidified by the addition of 1 microL 1% (v/v) trifluoroacetic acid (TFA). All liquid dispensing was done using an I-DOT One instrument.
Liquid chromatography: For the HRMS1-DIA experiments and the DIA isolation window survey, Evosep One liquid chromatography was used. The standard 31-minute or 58-minute pre-defined Whisper gradients were used with a flow rate of 100 nl/min for peptide elution.
Mass spectrometry: The mass spectrometer was operated in positive mode with the FAIMSPro interface compensation voltage set to -45 V. MS1 scans were carried out at 120,000 resolution with an automatic gain control (AGC) of 300% and maximum injection time set to auto. For the DIA isolation window survey, a scan range of 500–900 was used, and 400–1000 rest of the experiments. Higher energy collisional dissociation (HCD) was used for precursor fragmentation with a normalized collision energy (NCE) of 33% and the MS2 scan AGC target was set to 1000%.
Raw data processing: The mESC raw data files were processed with Spectronaut 17.

Data collection

The data were provided by the Author and is accessible at the Dataverse The folder ('20240205_111248_mESC_SNEcombine_m15-m2i/') contains the following files of interest:

⁠20240205_111251_PEPQuant (Normal).tsv⁠: the PSM level data
⁠20240205_111251_Peptide Quant (Normal).tsv⁠: the peptide level data
⁠20240205_111251_PGQuant (Normal).tsv⁠: the protein level data

The metadata were downloaded from the Zenodo repository.

sample_facs.csv: the metadata

We formatted the quantification table so that columns match with the metadata. Then, both tables are then combined in a single QFeatures object using the scp::readSCP() function.

The peptide data were formated to a SingleCellExperiment object and the sample metadata were matched to the column names and stored in the colData. The object is then added to the QFeatures object and the rows of the PSM data are linked to the rows of the peptide data based on the peptide sequence information through an AssayLink object.

The protein data were formated to a SingleCellExperiment object and the sample metadata were matched to the column names and stored in the colData. The object is then added to the QFeatures object and the rows of the peptide data are linked to the rows of the protein data based on the protein sequence information through an AssayLink object.

Source

The peptide and protein data can be downloaded from the Dataverse The raw data and the quantification data can also be found in the MassIVE repository MSV000092429: ftp://MSV000092429@massive.ucsd.edu/.

References

Source article: Petrosius, V., Aragon-Fernandez, P., Üresin, N. et al. "Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition." Nat Commun 14, 5910 (2023). (link to article).