bubis2025 Astral

R/bubis2025_astral.R

@@ -0,0 +1,131 @@
+##' Bubis et al. 2023 (Nat Methods): Challenging the Astral mass analyzer.
+##'
+##' Single-cell (or single-cell range peptide dilution) proteomics data
+##' acquired on the Thermo Scientific Orbitrap Astral mass spectrometer.
+##' The dataset contains single-cell range peptide dilution from Hela or
+##' K562 cell lines, single-cell data from A549 and H460 cell lines
+##' (epithelial-like human lung cancer cells), as well as trophectoderm-
+##' like (TE-like) and naive human pluripotent stem (hPS) cells. The
+##' dataset contains quantitative information at the PSM, peptide and
+##' protein levels. The raw data were analysed using Spectronaut version
+##' 18.
+##'
+##' @format A [QFeatures] object with 602 sets, each set being a
+##' [SingleCellExperiment] object:
+##'
+##' - Sets 1-594: PSM data from the Spectronaut peptides report files
+##'   with LFQ quantities from the `PEP.MS1Quantity` column.
+##' - Sets 595-598: Peptide data resulting from the PSM to peptide
+##'   aggregation of the 594 PSM set. Resulting peptide sets were
+##'   joined into assay sets based on the figure they were used for (1,
+##'   2, 4 or 5).
+##' - Sets 599-602: Protein data from the Spectronaut protein report
+##'   files with LFQ quantities from the `PG.Quantity` column.
+##'
+##' The `colData(bubis2025())` contains cell type annotation, search
+##' strategy, LC method throughput, FAIMS compensation voltage and figure
+##' in which the sample was used. The description of the `rowData` fields
+##' can be found in the [`Spectronaut` user manual](https://biognosys.com/content/uploads/2025/06/Spectronaut-20-Manual.pdf).
+##'
+##' @section Acquisition protocol:
+##'
+##' The data were acquired using the following setup. More information
+##' can be found in the source article (see *References*).
+##'
+##' - **Cell isolation**: A549 and H460 cells were isolated into 384-well
+##'   plates using the cellenONE robot. TE-like cells and hSP cells were
+##'   sorted into 384-well plates using the FACS Aria III (BD) controlled
+##'   by the DiVa software version 9.0.1. TE-like cells were selected
+##'   based on their TROP2 positivity while naive hPS cells were selected
+##'   based on their SUSD2 positivity. Whether cells were sorted using
+##'   cellenONE or FACS, the wells were pre-filled with 1 microL of
+##'   lysis/digestion buffer.
+##' - **Sample preparation** Lysis and digestion were performed in the
+##'   plates for 30 min at 50°C, then stopped by adding 0.1% TFA. Liquid
+##'   dispensing was performed using the cellenONE robot. The plates were
+##'   stored at -20°C until injection.
+##' - **Liquid chromatography**: Samples were injected directly from the
+##'   384-well plate. Chromatographic separation of peptides was
+##'   performed on a vanquish Neo UHPLC system connected to an Aurora
+##'   Ultimate TS 25-cm nanoflow UHPLC column with an integrated emitter
+##'   (Ion Optics) at 50 °C in direct injection mode. Peptide separation
+##'   was performed at 30-80 SPD, with details provided in the `colData`
+##'   for each sample.
+##' - **Mass spectrometry**: Acquisition was conducted using an Orbitrap
+##'   Astral mass spectrometer equipped with the FAIMS Pro or FAIMS Pro
+##'   Duo interface and an EASY-Spray source. FAIMS compensation voltage
+##'   (CV) was set to -48 V except for the samples used in fig. 2, for
+##'   which different CV were tested. The exact CV used for each sample
+##'   is specified in the `colData`. MS1 spectra were recorded using the
+##'   Orbitrap analyser at a resolution of 240,000, from m/z 400 to 900,
+##'   using an automated gain control (AGC) target of 500 % and a maximum
+##'   injection time of 100 ms. For MS2 in DIA mode using the Astral
+##'   analyzer, non-overlapping isolation windows of 20 m/z. A scan range
+##'   of m/z 400 to 800 was selected. Precursor accumulation time was set
+##'   to 60 ms and the AGC target to 800%.
+##' - **Raw data processing**: Raw files were processed using
+##'   Spectronaut version 18.6.231227.55695. For results marked as
+##'   ‘method evaluation’, DirectDIA+ was used in method evaluation mode
+##'   without cross-normalisation. ‘DirectDIA+’ indicates that results
+##'   were analyzed in DirectDIA+ mode. For library searches, higher-
+##'   input DIA recorded results were first analyzed in DirectDIA+ mode,
+##'   and a library was created from those files using Spectronaut.
+##'   Quantification was performed at the MS1 level. Carbamidomethylation
+##'   of cysteines as a static modification was removed for single-cell
+##'   searches. Factory settings were used for all analyses and for
+##'   library generation unless otherwise indicated. ‘Optimized settings’
+##'   (OS) indicates that searches were performed with a more stringent
+##'   cutoff value of 0.01. The search strategy used for each sample is
+##'   specified in the `colData`. Searches were performed against the
+##'   human proteome (UniProt proteome UP000005640) and the CRAPome.
+##'
+##' @section Data collection:
+##'
+##' The MS raw proteomics data, Spectronaut search results and fasta
+##' files used are available on the ProteomeXchange Consortium via the
+##' PRIDE partner repository with the dataset identifier [PXD049412](https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD049412).
+##' Only files related to single-cells or single-cell range peptide
+##' dilutions were used for this dataset (fig. 1, 2, 4 and 5). Sample
+##' annotations were manually generated using the file names and
+##' descriptions from the source article.
+##'
+##' PSM and proteins data were extracted from the
+##' `_Report_Peptides_JB_Pivot.tsv` and `_Report_Protein_JB_Pivot.tsv`
+##' files respectively.
+##'
+##' Sample annotations and PSM features tables were combined in a single
+##' [QFeatures] object using the [scp::readSCP()] function. Peptide data
+##' were obtained by aggregating PSM data to the peptide level. Resulting
+##' peptides sets were joined according to the figure for which they were
+##' used in the source article. Individual peptides sets were discarded.
+##' Protein data were made in a separate [QFeatures] object, and sets
+##' were joined based on the figure they are related to. Combined sets
+##' were added to the first [QFeatures] object containing PSM and peptide
+##' data, and links between peptide and protein sets were set manually.
+##'
+##' Note that the [QFeatures] object has not been further processed and
+##' has therefore not been normalized, log-transformed or batch-
+##' corrected.
+##'
+##' @source The PSM and protein data, as well as sample annotations, can
+##'     be downloaded on the ProteomeXchange Consortium via the PRIDE
+##'     partner repository with the dataset identifier [PXD049412](https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD049412).
+##'
+##' @references
+##'
+##' Julia A. Bubis, Tabiwang N. Arrey, Eugen Damoc, Bernard Delanghe,
+##' Jana Slovakova, Theresa M. Sommer, Harunobu Kagawa, Peter Pichler,
+##' Nicolas Rivron, Karl Mechtler and Manuel Matzinger.
+##'
+##' 2025. "Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity"
+##' Nature Methods  https://doi.org/10.1038/s41592-024-02559-1
+##' DOI:[10.1038/s41592-024-02559-1](https://doi.org/10.1038/s41592-024-02559-1)
+##'
+##' @examples
+##' \donttest{
+##' bubis2025()
+##' }
+##'
+##' @keywords datasets
+##'
+"bubis2025"

inst/extdata/metadata.csv

@@ -29,4 +29,8 @@
 "hu2023_K562","Single-cell proteomics data of K562 cells","3.19",NA,"TXT","ftp://massive.ucsd.edu/MSV000089625/",NA,"Homo sapiens",9606,TRUE,"MassIVE","Enes Sefa Ayar <enes.ayar@uclouvain.be>","SingleCellExperiment","Rda","scpdata/hu2023_K562.Rda",2024-10-24,1,"Proteome Discoverer","LFQ",FALSE,FALSE,TRUE,TRUE,NA
 "hu2023_oocyte","Single-cell proteomics data of oocytes","3.19",NA,"TXT","ftp://massive.ucsd.edu/MSV000089625/",NA,"Homo sapiens",9606,TRUE,"MassIVE","Enes Sefa Ayar <enes.ayar@uclouvain.be>","SingleCellExperiment","Rda","scpdata/hu2023_oocyte.Rda",2024-10-24,1,"Proteome Discoverer","LFQ",FALSE,FALSE,TRUE,TRUE,NA
 "ai2025a","Single-cell proteomics data of adult cardiomyocytes from Ai et al. (2025)","3.21",NA,"TXT","ftp://massive.ucsd.edu/v07/MSV000094438/updates/2024-10-23_bineka_5deafa61/other/Supplementary%20Files/aCMs/report.tsv",NA,"Homo sapiens",9606,TRUE,"MassIVE","Laurent Gatto <laurent.gatto@uclouvain.be>","QFeatures","Rda","scpdata/ai2025a.rda",2025-02-22,304,"DIA-NN","LFQ",TRUE,TRUE,TRUE,TRUE,"DIA-NN output retrieved using MsDataHub::Ai2025_aCMs_report.tsv()"
+<<<<<<< master
+"bubis2025","Single-cell proteomics data of HeLa, K562, A549, H460, TE-like and hPS cells acquired on the Astral MS.","3.21",NA,"TXT","https://www.ebi.ac.uk/pride/archive/projects/PXD049412",NA,"Homo sapiens",9606,TRUE,"MassIVE","Samuel Gregoire <samuel.gregoire@uclouvain.be>","QFeatures","Rda","scpdata/bubis2025.Rda",2025-08-19,602,"Spectronaut","LFQ",TRUE,TRUE,TRUE,TRUE,NA
+=======
 "wu2026","Label-free single-cell proteomics data from prenatal human brain tissue (gestational weeks 13, 15, and 19) from Wu et al. (2026)","3.22",NA,"TXT","https://www.ebi.ac.uk/pride/archive/projects/PXD071075",NA,"Homo sapiens",9606,TRUE,"PRIDE","Léopold Guyot <leopoldguyot@uclouvain.be>","QFeatures","Rda","scpdata/wu2026.rda",2026-01-27,2313,"DIA-NN","LFQ",TRUE,TRUE,TRUE,TRUE,"DIA-NN output retrieved from PRIDE repository accession PXD071075"
+>>>>>>> master