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lgatto committed Apr 11, 2024
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####---- petrosius2023_mES ----####

##' Petrosius et al, 2023 (Nat. Comm.): Mouse embryonic stem cell (mESC) in
##' 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
##' 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.
##'
##'
##' @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
##' - 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.
##' peptides and 603 single-cells.
##' - `proteins`: protein data containing quantitative data for 4270
##' proteins and 603 single-cells.
##' proteins and 603 single-cells.
##'
##' Sample annotation is stored in `colData(petrosius2023_mES())`.
##'
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##' 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 μm sorting chip. Cells were sorted at single-cell resolution,
##' into a 384-well Eppendorf LoBind PCR plate (Eppendorf AG) containing 1 μL
##' - **Sample isolation**: Cell sorting was done on a Sony MA900 cell sorter
##' using a 130 μm sorting chip. Cells were sorted at single-cell resolution,
##' into a 384-well Eppendorf LoBind PCR plate (Eppendorf AG) containing 1 μL
##' of lysis buffer.
##' - **Sample preparation**: Single-cell protein lysates were digested with
##' 2 ng of Trypsin (Sigma cat. Nr. T6567) supplied in 1 μL of digestion
##' - **Sample preparation**: Single-cell protein lysates were digested with
##' 2 ng of Trypsin (Sigma cat. Nr. T6567) supplied in 1 μL of digestion
##' buffer (100mM TEAB pH 8.5, 1:5000 (v/v) benzonase (Sigma cat. Nr. E1014)).
##' The digestion was carried out overnight at 37 °C, and subsequently
##' acidified by the addition of 1 μL 1% (v/v) trifluoroacetic acid (TFA).
##' The digestion was carried out overnight at 37 °C, and subsequently
##' acidified by the addition of 1 μL 1% (v/v) trifluoroacetic acid (TFA).
##' All liquid dispensing was done using an I-DOT One instrument (Dispendix).
##' - **Liquid chromatography**: The Evosep one liquid chromatography system was
##' - **Liquid chromatography**: The Evosep one liquid chromatography system was
##' used for DIA isolation window survey and HRMS1-DIA experiments.The standard
##' 31 min or 58min pre-defined Whisper gradients were used, where peptide
##' elution is carried out with 100 nl/min flow rate. A 15 cm × 75 μm
##' ID column (PepSep) with 1.9 μm C18 beads (Dr. Maisch, Germany) and a 10
##' μm ID silica electrospray emitter (PepSep) was used. Both LC systems were
##' coupled online to an orbitrap Eclipse TribridMass Spectrometer
##' (ThermoFisher Scientific) via an EasySpray ion source connected to a
##' 31 min or 58min pre-defined Whisper gradients were used, where peptide
##' elution is carried out with 100 nl/min flow rate. A 15 cm × 75 μm
##' ID column (PepSep) with 1.9 μm C18 beads (Dr. Maisch, Germany) and a 10
##' μm ID silica electrospray emitter (PepSep) was used. Both LC systems were
##' coupled online to an orbitrap Eclipse TribridMass Spectrometer
##' (ThermoFisher Scientific) via an EasySpray ion source connected to a
##' FAIMSPro device.
##' - **Mass spectrometry**: The mass spectrometer was operated in positive
##' - **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 MS2 scan AGC target was set to 1000%.
##' - **Raw data processing**: The mESC raw data files were processed with
##' Spectronaut 17 and protein abundance tables exported and analyzed further
##' with python.
##' 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 MS2 scan AGC target was set to 1000%.
##' - **Raw data processing**: The mESC raw data files were processed with
##' Spectronaut 17 and protein abundance tables exported and analyzed further
##' with python.
##'
##' @section Data collection:
##'
##' The data were provided by the Author and is accessible at the [Dataverse]
##' (https://dataverse.uclouvain.be/dataset.xhtml?persistentId=doi:10.14428/DVN/EMAVLT)
##' The folder ('20240205_111248_mESC_SNEcombine_m15-m2i/') contains the
##' 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] (https://zenodo.org/records/8146605).
##'
##' The metadata were downloaded from the [Zenodo repository](https://zenodo.org/records/8146605).
##'
##' - `sample_facs.csv`: the metadata
##'
##' We formatted the quantification table so that columns match with the
##'
##' 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
##'
##' 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
##' 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
##'
##' 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
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##' The raw data and the quantification data can also be found in the
##' MassIVE repository `MSV000092429`:
##' ftp://[email protected]/.
##'
##'
##' @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).
##' **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](https://doi.org/10.1038/s41467-023-41602-1)).
##'
##' @examples
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