derks2022: Derks et al. 2022 - plexDIA (Nat. Biotechnol.): PDAC vs...

In UCLouvain-CBIO/scpdata: Single-Cell Proteomics Data Package

Derks et al. 2022 - plexDIA (Nat. Biotechnol.): PDAC vs melanoma cells vs monocytes

Description

Single cell proteomics data acquired by the Slavov Lab using the plexDIA protocol. It contains quantitative information from pancreatic ductal acinar cells (PDAC; HPAF-II), melanoma cells (WM989-A6-G3) and monocytes (U-937) at precursor and protein level. The each run acquired 3 samples thanks to mTRAQ multiplexing.

Usage

derks2022

Format

A QFeatures object with 66 assays, each assay being a SingleCellExperiment object. The assays either hold the DIA-NN main output report table or the DIA-NN MS1 extracted signal table. The DIA-NN main output report table contains the results of the spectrum identification and quantification. The DIA-NN MS1 extracted signal table contains quantification for all mTRAQ channels if its precursors was identified in at least one of the channels, regardless of whether there is sufficient evidence in those channels at 1% FDR.

The data is composed of three datasets

1. Bulk: dataset containing bulk (100-cell) data acquired using a Q-Exactive mass spectrometer. Assays 1-3 contain data from the DIA-NN main output report; assay 4 is the DIA-NN MS1 extracted signal.

2. tims: dataset containing single-cell data acquired using a timsTOF-SCP mass spectrometer. Assays 5-15 contain data from the DIA-NN main output report; assay 16 is the DIA-NN MS1 extracted signal.

3. qe: dataset containing single-cell data acquired using a Q-Exactive mass spectrometer. Assays 17-64 contain data from the DIA-NN main output report; assay 65 is the DIA-NN MS1 extracted signal.

The last assay proteins contains the processed protein data table generated by the authors.

The colData(derks2022()) contains cell type annotations and batch annotations. The description of the rowData fields for the different assays can be found in the DIA-NN documentation.

Acquisition protocol

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

• Cell isolation: CellenONE cell sorting.

• Sample preparation performed using the improved SCoPE2 protocol using the CellenONE liquid handling system. nPOP cell lysis (DMSO) + trypsin digestion + mTRAQ (3plex) labelling and pooling. A target library was generated as well to perform prioritized DDA (Huffman et al. 2022) using MaxQuant.Live (2.0.3).

• Separation: bulk - online nLC (Dionex UltiMate 3000 UHPLC) with a 25 cm × 75 µm IonOpticks Aurora Series UHPLC column (AUR2-25075C18A), 200nL/min. qe - online nLC (Dionex UltiMate 3000 UHPLC) with a 15 cm × 75 µm IonOpticks Aurora Series UHPLC column (AUR2-15075C18A), 200nL/min. tims - nanoElute liquid chromatography system (Bruker Daltonics) using a 25 cm × 75 µm, 1.6-µm C18 (AUR2-25075C18A-CSI, IonOpticks).

• Ionization: ESI.

• Mass spectrometry: cf article.

• Data analysis: DIA-NN (1.8.1 beta 16).

Data collection

The data were collected from a shared Google Drive folder that is accessible from the SlavovLab website (see Source section).

For each dataset separately, we combined the sample annotation and the DIANN tables in a QFeatures object following the scp data structure. We then combined the three datasets in a single QFeatures object. We load the proteins table processed by the authors as a SingleCellExperiment object and adapted the sample names to match those in the QFeatures object. We 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 the Slavov Lab website. The raw data and the quantification data can also be found in the massIVE repository MSV000089093.

References

Derks, Jason, Andrew Leduc, Georg Wallmann, R. Gray Huffman, Matthew Willetts, Saad Khan, Harrison Specht, Markus Ralser, Vadim Demichev, and Nikolai Slavov. 2022. "Increasing the Throughput of Sensitive Proteomics by plexDIA." Nature Biotechnology, July. Link to article

Examples

derks2022()

UCLouvain-CBIO/scpdata documentation built on Oct. 29, 2024, 4:22 p.m.