Merge pull request #29 from EnesSefaAyar/master

khan2023() correction and new datasets

R/hu2023.R

@@ -0,0 +1,106 @@
+##' Hu et al, 2023 (The Journal of Physical Chemistry B): Correlated protein modules
+##'
+##' @description
+##'
+##' They demonstrate the correlations between the levels of pairs of proteins 
+##' in single-cell proteomics (SCP) at steady state. In measuring pairwise 
+##' correlations among 1000 proteins in a population of K562 cells and oocytes, 
+##' they observed many correlated protein modules (CPMs) that are functionally 
+##' involved in certain biological functions. Certain CPMs are specific to a 
+##' particular cell type, some common to different cell types. Additionally, 
+##' compared to single-cell transcriptomics and bulk proteomics, 
+##' protein correlations are functionally and experimentally more significant 
+##' in SCP than those corresponding mRNAs.
+##'
+##' @format Two [SingleCellExperiment] objects:
+##'
+##' - `proteins_K562`: protein data containing quantitative data for 1249
+##'   proteins and 69 single-cells with zero imputation.
+##' - `proteins_oocyte`: protein data containing quantitative data for 3422
+##'   proteins and 137 single-cells with zero imputation.
+##'
+##' The `colData(hu2023_oocyte())` contains cell type annotation.
+##' The `colData(hu2023_K562())` contains cell type annotation.
+##'
+##' @section Acquisition protocol:
+##'
+##' The data were acquired using the following setup. More information
+##' can be found in the source article (see `References`).
+##'
+##' - **Cell isolation**: K562 cells were re-suspended and washed in cold PBS. 
+##'   Single cells/10 cells were sorted into 96-well plates using a FACSAria 
+##'   instrument. Oocyte-cumulus complexes from C57/6J mice were collected 
+##'   after PMSG and HCG injections, with hyaluronidase used to remove cumulus 
+##'   cells. All samples stored at -80 degrees Celsius.
+##' - **Sample preparation** Cells were digested with trypsin at 37 degrees 
+##'   Celsius for 3 hours. For label-free proteomics, digestion was terminated 
+##'   by adding 0.43% TFA and 1% ACN in water, followed by drying in a 
+##'   concentrator. Peptides were resuspended in 0.1% TFA and 1% ACN, and 
+##'   then transferred to sample tubes for LC-MS/MS analysis.
+##' - **Separation**: 4 microliters of peptide digests were injected into a 
+##'   high-performance chromatography column (IonOpticks) and separated at a 
+##'   flow rate of 100 nL/min using a nanoflow liquid chromatography system. 
+##'   The effective gradient was 70 mins, allowing 16 cells per day.
+##' - **Ionization**: Peptides were analyzed using an Orbitrap Eclipse mass 
+##'   spectrometer with a FAIMS Pro interface. FAIMS compensation voltages of 
+##'   −55 and −70 V were applied, with a 1-second cycle time for both voltages.
+##' - **Mass spectrometry**: MS spectra were acquired with the Orbitrap 
+##'   analyzer, while MS/MS spectra were acquired with a linear ion trap 
+##'   analyzer. The maximum ion injection time for MS/MS was 200 ms.
+##' - **Data analysis**: MS raw files were searched against the UniProt 
+##'   human protein database and an in-house contamination database 
+##'   using Proteome Discoverer(2.4). Label-free quantification was based on 
+##'   peak intensity with the match-between-runs (MBR) feature enabled.
+##'
+##' @section Data collection:
+##'
+##' The oocyte protein data shared by the author and it is accessible from the 
+##' [Shared File](https://biopic-my.sharepoint.cn/:x:/g/personal/humo_biopic_pku_edu_cn/EfX4CHedVopLuSx2OJNj6LABdESGNdKz4Eh8Zawvd-fNNQ?e=E5m09k&xsdata=MDV8MDJ8ZW5lcy5heWFyQHVjbG91dmFpbi5iZXxjYjY2M2MwYzNjMDY0YjZhNjc1NTA4ZGM4YzMzNjc1YXw3YWIwOTBkNGZhMmU0ZWNmYmM3YzQxMjdiNGQ1ODJlY3wxfDB8NjM4NTM5Mzk5NjI1Mzg1NDQ3fFVua25vd258VFdGcGJHWnNiM2Q4ZXlKV0lqb2lNQzR3TGpBd01EQWlMQ0pRSWpvaVYybHVNeklpTENKQlRpSTZJazFoYVd3aUxDSlhWQ0k2TW4wPXwwfHx8&sdata=Zmt4YnZFZFViTitJRkdTc0FTK2thMjdTT0EzV2JJeS83WlZmV3R6SzdvRT0%3d)
+##' The K563 protein data is accessible from the
+##' [GitHub] https://github.com/dionezhang/CPM/blob/master/ProteinAbundance.Rdata 
+##'
+##' - `DataMatrix-oocyte-20240614.csv`: normalized imputed protein matrix
+##' - `ProteinAbundance.Rdata`: protein matrices (normalized, log transformed) 
+##'
+##' We initialized an empty QFeatures object and added the corresponding 
+##' protein assays as [SingleCellExperiment] objects.
+##'
+##' The oocyte protein data were exported from the shared link as 
+##' (`DataMatrix-oocyte-20240614.csv`). The data were formatted to a 
+##' [SingleCellExperiment] object and the SampleType information were added 
+##' as only metadata, and stored in the `colData`. The object is then added 
+##' to the [QFeatures] object.
+##'
+##' The 562 cells protein data were downloaded from the GitHub link and loaded
+##' to the memory. The `Norm` object were formatted to a [SingleCellExperiment] 
+##' object and the SampleType information were added as only metadata, and 
+##' stored in the `colData`. The object is then added to the [QFeatures] object.
+##'
+##' @source
+##' The oocyte data were downloaded from the
+##' [Shared File](https://biopic-my.sharepoint.cn/:x:/g/personal/humo_biopic_pku_edu_cn/EfX4CHedVopLuSx2OJNj6LABdESGNdKz4Eh8Zawvd-fNNQ?e=E5m09k&xsdata=MDV8MDJ8ZW5lcy5heWFyQHVjbG91dmFpbi5iZXxjYjY2M2MwYzNjMDY0YjZhNjc1NTA4ZGM4YzMzNjc1YXw3YWIwOTBkNGZhMmU0ZWNmYmM3YzQxMjdiNGQ1ODJlY3wxfDB8NjM4NTM5Mzk5NjI1Mzg1NDQ3fFVua25vd258VFdGcGJHWnNiM2Q4ZXlKV0lqb2lNQzR3TGpBd01EQWlMQ0pRSWpvaVYybHVNeklpTENKQlRpSTZJazFoYVd3aUxDSlhWQ0k2TW4wPXwwfHx8&sdata=Zmt4YnZFZFViTitJRkdTc0FTK2thMjdTT0EzV2JJeS83WlZmV3R6SzdvRT0%3d)
+##' The K563 cells protein data downloaded from the
+##' [GitHub] https://github.com/dionezhang/CPM/blob/master/ProteinAbundance.Rdata 
+##' The raw data and the quantification data can also be found in the
+##' MassIVE repository `MSV000089625`:
+##' ftp://[email protected]/.
+##'
+##' @references
+##' Hu, M., Zhang, Y., Yuan, Y., Ma, W., Zheng, Y., Gu, Q., & Xie, X. S. 2023.
+##' “Correlated protein modules revealing functional coordination of interacting
+##' proteins are detected by single-cell proteomics.”. The Journal of Physical
+##' Chemistry B,
+##' ([link to article](https://doi.org/10.1021/acs.jpcb.3c00014)).
+##'
+##' @aliases hu2023_K562 
+##' @aliases hu2023_oocyte
+##'
+##' @examples
+##' \donttest{
+##' hu2023_oocyte()
+##' hu2023_K562()
+##' }
+##'
+##' @keywords datasets
+##'
+"hu2023"

R/khan2023.R

@@ -20,10 +20,10 @@
 ##'   empty (negative control) channels and unused channels.
 ##' - `peptides`: peptide data containing quantitative data for 10055
 ##'   peptides and 421 single-cells.
-##' - `proteins_imputed`: protein data containing quantitative data for 4096
-##'   proteins and 421 single-cells with k-nearest neighbors (KNN) imputation.
-##' - `proteins_unimputed`: protein data containing quantitative data for 4096
-##'   proteins and 421 single-cells without imputation.
+##' - `proteins_imputed`: protein data containing quantitative data for 4571
+##'   proteins and 420 single-cells with k-nearest neighbors (KNN) imputation.
+##' - `proteins_unimputed`: protein data containing quantitative data for 4571
+##'   proteins and 420 single-cells without imputation.
 ##'
 ##' The `colData(khan2023())` contains cell type and batch annotations that
 ##' are common to all assays. The description of the `rowData` fields for the
@@ -73,7 +73,7 @@
 ##' based on the peptide sequence information through an `AssayLink` object.
 ##'
 ##' The imputed protein data were taken from the same google drive folder
-##' (`EpiToMesen.TGFB.nPoP_trial1_ProtByCellMatrix_NSThreshDART_medIntCrNorm_imputedNotBC.csv`).
+##' (`EpiToMesen.TGFB.nPoP_trial1_1PercDartFDRTMTBulkDIA.WallE_imputed.txt`).
 ##' The data were formatted to a [SingleCellExperiment] object and the sample
 ##' metadata were matched to the column names (mapping is retrieved
 ##' after running the SCoPE2 R script, `EMTTGFB_singleCellProcessing.R`) and
@@ -82,7 +82,7 @@
 ##' based on the protein sequence information through an `AssayLink` object.
 ##'
 ##' The unimputed protein data were taken from the same google drive folder
-##' (`EpiToMesen.TGFB.nPoP_trial1_ProtByCellMatrix_NSThreshDART_medIntCrNorm_unimputed.csv`).
+##' (`EpiToMesen.TGFB.nPoP_trial1_1PercDartFDRTMTBulkDIA.WallE_unimputed.txt`).
 ##' The data were formatted and added exactly as imputed data.
 ##'
 ##' @source
@@ -97,8 +97,8 @@
 ##' @references
 ##' Saad Khan, Rachel Conover, Anand R. Asthagiri, Nikolai Slavov. 2023.
 ##' "Dynamics of single-cell protein covariation during epithelial–mesenchymal
-##' transition." bioRxiv.
-##' ([link to article](https://doi.org/10.1101/2023.12.21.572913)).
+##' transition." Journal of Proteome Research.
+##' ([link to article](https://pubs.acs.org/doi/10.1021/acs.jproteome.4c00277)).
 ##'
 ##' @examples
 ##' \donttest{

R/krull2024.R

@@ -0,0 +1,84 @@
+##' Krull et al, 2024 (Nature Communications): IFN-γ response
+##'
+##' They develop a new strategy for data-independent acquisition (DIA) that 
+##' leverages the co-analysis of low-input samples alongside a corresponding 
+##' enhancer (ME) of higher input. Using DIA-ME, they investigate the 
+##' proteomic response of U-2 OS cells to interferon gamma (IFN-y) at 
+##' the single-cell level.
+##'
+##' @format A [QFeatures] object with 159 assays, each assay being a
+##' [SingleCellExperiment] object.
+##'
+##' - Assay 1-158: DIA-NN main output report table split for each
+##'   acquisition run. First 15 run acquires 10 single cells (MEs) and, 
+##'   remaining 143 run acquires 1 single cell. It contains the results
+##'   of the spectrum identification and quantification.
+##' - `proteins`: DIA-NN protein group matrix, containing normalised
+##'   quantities for 1553 protein groups in 143 single cells. Proteins
+##'   are filtered at (Q.Value <= 0.01), (Lib.Q.Value <= 0.01), and 
+##'   (Lib.PG.Q.Value <= 0.01).
+##'   
+##' The `colData(krull2024())` contains cell type annotations. The description 
+##' of the `rowData` fields for the different assays can be found in the
+##' [`DIA-NN` documentation](https://github.com/vdemichev/DiaNN#readme).
+##'
+##' @section 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 digestion, followed 
+##'   by dilution in 1.5 mL PBS, and isolated using BD FACSAria III instrument.
+##' - **Sample preparation**: Sorted single cells were collected in lysis 
+##'   buffer (50 mM TEAB, pH 8.5, and 0.025% DDM), denatured at 70 degrees 
+##'   Celsius for 30 minutes. Samples were acidified with 0.5% FA and 
+##'   transferred to auto sampler plates for mass spectrometry analysis.
+##' - **Separation**: Peptides were injected in a 2 microliter volume onto 
+##'   a (25 cm x 75  micrometer) ID column at a flow rate of 300 nL/min, 
+##'   separated using a gradient of ACN in water with 0.1% FA over 15 minutes, 
+##'   connected to a nano-ESI source.
+##' - **Ionization**: Ionization was performed using a 1,500 V capillary 
+##'   voltage with 3.0 L/min dry gas and a dry temperature of 180 degrees 
+##'   Celsius. MS data acquisition was conducted in diaPASEF mode using a 
+##'   timsTOF Pro mass spectrometer.
+##' - **Mass spectrometry**: MS1 scans covered a range of 200-1,700 m/z, 
+##'   while DIA window isolation targeted 475-1,000 m/z with eight DIA scans 
+##'   per cycle. Fragmentation was triggered by collision energy ranging from 
+##'   45 eV to 27 eV depending on the ion mobility.
+##' - **Data analysis**: Data was processed using DIA-NN (v1.8.0) and 
+##'   Spectronaut 18 in a library-free approach, using deep learning 
+##'   for spectrum prediction, retention times, and ion mobility.
+##'
+##' @section Data collection:
+##'
+##' The data were collected from the PRIDE
+##' [repository](https://www.ebi.ac.uk/pride/archive/projects/PXD053464)
+##' in the `03_SingleCell_Searches.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, 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](https://www.ebi.ac.uk/pride/archive/projects/PXD053464)
+##' with accession ID `PXD053464`.
+##'
+##' @references
+##' Krull, K. K., Ali, S. A., & Krijgsveld, J. 2024. "Enhanced feature matching
+##' in single-cell proteomics characterizes IFN-γ response and co-existence of
+##' Cell States." Nature Communications, 15(1). 
+##' [Link to article](https://doi.org/10.1038/s41467-024-52605-x) 
+##' 
+##' @examples
+##' \donttest{
+##' krull2024()
+##' }
+##'
+##' @keywords datasets
+##'
+"krull2024"

inst/extdata/metadata.csv

@@ -25,3 +25,6 @@
 "guise2024","Single-cell proteomics data of 108 postmortem CTL or ALS spinal moto neurons","3.19",NA,"TXT","ftp://massive.ucsd.edu/v05/MSV000092119/",NA,"Homo sapiens",9606,TRUE,"MassIVE","Christophe Vanderaa <[email protected]>","QFeatures","Rda","scpdata/guise2024.rda",2024-01-05,47,"Proteome Discoverer","LFQ",TRUE,TRUE,TRUE,TRUE,NA
 "petrosius2023_mES","Mouse embryonic stem cells across ground-state (m2i) and differentiation-permissive (m15) culture conditions.","3.19",NA,"TXT","https://dataverse.uclouvain.be/dataset.xhtml?persistentId=doi:10.14428/DVN/EMAVLT",NA,"Homo sapiens",9606,TRUE,"Dataverse","Enes Sefa Ayar <[email protected]>","QFeatures","Rda","scpdata/petrosius2023_mES.Rda",2024-04-09,605,"Spectronaut","LFQ",TRUE,TRUE,TRUE,TRUE,NA
 "petrosius2023_AstralAML","Single-cell proteomics data of 4 cell types from the OCI-AML8227 model.","3.19",NA,"TXT","https://dataverse.uclouvain.be/dataset.xhtml?persistentId=doi:10.14428/DVN/4DSPJM",NA,"Homo sapiens",9606,TRUE,"Dataverse","Samuel Gregoire <[email protected]>","QFeatures","Rda","scpdata/petrosius2023_AstralAML.Rda",2023-06-08,217,"Spectronaut","LFQ",TRUE,TRUE,TRUE,TRUE,NA
+"krull2024","Single-cell proteomics data IFN-γ response of U-2 OS cells","3.19",NA,"TXT","https://www.ebi.ac.uk/pride/archive/projects/PXD053464",NA,"Homo sapiens",9606,TRUE,"PRIDE","Enes Sefa Ayar <[email protected]>","QFeatures","Rda","scpdata/krull2024.Rda",2024-10-24,159,"DIA-NN","LFQ",TRUE,FALSE,TRUE,TRUE,NA
+"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 <[email protected]>","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 <[email protected]>","SingleCellExperiment","Rda","scpdata/hu2023_oocyte.Rda",2024-10-24,1,"Proteome Discoverer","LFQ",FALSE,FALSE,TRUE,TRUE,NA

inst/scripts/make-data_hu2023_K562.R

@@ -0,0 +1,43 @@
+
+####---- Hu et al, 2023 ---####
+
+
+## Hu, M., Zhang, Y., Yuan, Y., Ma, W., Zheng, Y., Gu, Q., & Xie, X. S. 2023. 
+## “Correlated protein modules revealing functional coordination of interacting 
+## proteins are detected by single-cell proteomics.”. The Journal of Physical 
+## Chemistry B, https://doi.org/10.1021/acs.jpcb.3c00014 
+
+library(SingleCellExperiment)
+library(scp)
+library(tidyverse)
+
+root <- "~/localdata/SCP/hu2023/"
+
+####---- Add the protein data ----####
+
+## Data accessible at GitHub repository
+## https://github.com/dionezhang/CPM/blob/master/ProteinAbundance.Rdata
+
+#### Load data ####
+load(paste0(root, "ProteinAbundance.Rdata"))
+
+Norm %>% 
+  mutate(X = rownames(Norm)) %>% 
+  readSingleCellExperiment(ecol = 1:69, fnames = "X") ->
+  K562
+
+## Protein data for K562 cells
+hu2023_K562 <- SingleCellExperiment(K562)
+
+prots <- rownames(hu2023_K562)
+rowData(hu2023_K562) <- Description[prots, ,drop = FALSE]
+rowData(hu2023_K562)$protein <- prots
+
+colData(hu2023_K562) <- DataFrame(row.names = colnames(Norm), 
+                           SampleType = rep("K562", length(colnames(Norm))))
+
+## Save data
+save(hu2023_K562,
+     file = file.path(paste0(root, "hu2023_K562.Rda")),
+     compress = "xz",
+     compression_level = 9)

inst/scripts/make-data_hu2023_oocyte.R

@@ -0,0 +1,39 @@
+
+####---- Hu et al, 2023 ---####
+
+
+## Hu, M., Zhang, Y., Yuan, Y., Ma, W., Zheng, Y., Gu, Q., & Xie, X. S. 2023. 
+## “Correlated protein modules revealing functional coordination of interacting 
+## proteins are detected by single-cell proteomics.”. The Journal of Physical 
+## Chemistry B, https://doi.org/10.1021/acs.jpcb.3c00014 
+
+library(SingleCellExperiment)
+library(scp)
+library(tidyverse)
+
+root <- "~/localdata/SCP/hu2023/"
+
+####---- Add the protein data ----####
+
+## Data shared by the author, and accessible at 
+## https://biopic-my.sharepoint.cn/:x:/g/personal/humo_biopic_pku_edu_cn/EfX4CHedVopLuSx2OJNj6LABdESGNdKz4Eh8Zawvd-fNNQ?rtime=7Xzb4B303Eg
+
+#### Load Data ####
+oocyte <- read.csv(paste0(root, "DataMatrix-oocyte-20240614.csv"))
+oocyte %>% 
+  rename(protein = X) %>% 
+  readSingleCellExperiment(ecol = 2:138, fnames = "protein") ->
+  oocyte
+
+## Protein data for oocytes
+hu2023_oocyte <- SingleCellExperiment(oocyte)
+
+colData(hu2023_oocyte) <- DataFrame(row.names = colnames(hu2023_oocyte), 
+                           SampleType = rep("oocyte", length(colnames(oocyte))))
+
+## Save data
+save(hu2023_oocyte,
+     file = file.path(paste0(root, "hu2023_oocyte.Rda")),
+     compress = "xz",
+     compression_level = 9)
+