specht2019v3: Specht et al. 2019 - SCoPE2 (biorRxiv): macrophages vs...
In UCLouvain-CBIO/scpdata: Single-Cell Proteomics Data Package

specht2019v3

R Documentation

Specht et al. 2019 - SCoPE2 (biorRxiv): macrophages vs monocytes (version 3)

Description

Single cell proteomics data acquired by the Slavov Lab. This is the version 3 of the data released in October 2020. It contains quantitative information of macrophages and monocytes at PSM, peptide and protein level.

Usage

specht2019v3

Format

A QFeatures object with 179 assays, each assay being a SingleCellExperiment object:

Assay 1-63: PSM data for SCoPE2 sets acquired with a TMT-11plex protocol, hence those assays contain 11 columns. Columns hold quantitative information from single-cell channels, carrier channels, reference channels, empty (blank) channels and unused channels.
Assay 64-177: PSM data for SCoPE2 sets acquired with a TMT-16plex protocol, hence those assays contain 16 columns. Columns hold quantitative information from single-cell channels, carrier channels, reference channels, empty (blank) channels and unused channels.
peptides: peptide data containing quantitative data for 9208 peptides and 1018 single-cells.
proteins: protein data containing quantitative data for 2772 proteins and 1018 single-cells.

The colData(specht2019v2()) contains cell type annotation and batch annotation that are common to all assays. The description of the rowData fields for the PSM data can be found in the MaxQuant documentation.

Acquisition protocol

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

Cell isolation: flow cytometry (BD FACSAria I).
Sample preparation performed using the SCoPE2 protocol. mPOP cell lysis + trypsin digestion + TMT-11plex or 16plex labeling and pooling.
Separation: online nLC (DionexUltiMate 3000 UHPLC with a 25cm x 75um IonOpticksAurora Series UHPLC column; 200nL/min).
Ionization: ESI (2,200V).
Mass spectrometry: Thermo Scientific Q-Exactive (MS1 resolution = 70,000; MS2 accumulation time = 300ms; MS2 resolution = 70,000).
Data analysis: DART-ID + MaxQuant (1.6.2.3).

Data collection

The PSM data were collected from a shared Google Drive folder that is accessible from the SlavovLab website (see Source section). The folder contains the following files of interest:

ev_updated_v2.txt: the MaxQuant/DART-ID output file
⁠annotation_fp60-97.csv⁠: sample annotation
⁠batch_fp60-97.csv⁠: batch annotation

We combined the sample annotation and the batch annotation in a single table. We also formatted the quantification table so that columns match with those of the annotation and filter only for single-cell runs. Both table are then combined in a single QFeatures object using the scp::readSCP() function.

The peptide data were taken from the Slavov lab directly (Peptides-raw.csv). It is provided as a spreadsheet. 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) and stored in the colData. The object is then added to the QFeatures object (containing the PSM assays) and the rows of the peptide data are linked to the rows of the PSM data based on the peptide sequence information through an AssayLink object.

The protein data (Proteins-processed.csv) is formatted similarly to the peptide data, and the rows of the proteins were mapped onto the rows of the peptide data based on the protein sequence information.

Note

Since version 2, a serious bug in the data were corrected for TMT channels 12 to 16. Many more cells are therefore contained in the data. Version 2 is maintained for backward compatibility. Although the final version of the article was published in 2021, we have kept specht2019v3 as the data set name for consistency with the previous data version specht2019v2.

Source

The data were downloaded from the Slavov Lab website via a shared Google Drive folder. The raw data and the quantification data can also be found in the massIVE repository MSV000083945: ftp://massive.ucsd.edu/MSV000083945.

References

Specht, Harrison, Edward Emmott, Aleksandra A. Petelski, R. Gray Huffman, David H. Perlman, Marco Serra, Peter Kharchenko, Antonius Koller, and Nikolai Slavov. 2021. "Single-Cell Proteomic and Transcriptomic Analysis of Macrophage Heterogeneity Using SCoPE2." Genome Biology 22 (1): 50. (link to article).