guise2024: Guise et al. 2020 (Cell Rep.): postmortem ALS spinal moto...

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

Guise et al. 2020 (Cell Rep.): postmortem ALS spinal moto neurons

Description

Single-cell proteomics data from postmortem human spinal moto neurons (MN) obtained from control donors or donors with amyotrophic lateral sclerosis (ALS). The data were generated following the NanoPOTS protocol. Cells were isolated from samples obtained by the university of Miami Brain Bank using laser capture microdissection (LCM). Additional information about the amount of TDP-43 intra-cellular levels has been assigned into levels 0 to 4.

Usage

guise2024

Format

A QFeatures object with 102 assays, each assay being a SingleCellExperiment object:

• ⁠F*⁠: 100 assays containing PSM data.

• peptides: quantitative data for 34,315 peptides in 108 samples. All samples combined, along with 8 additional unannotated samples.

• proteins: quantitative data for 4,437 protein groups in 108 samples. All samples combined, along with 8 additional unannotated samples.

Sample annotation is stored in colData(guise2024()).

Acquisition protocol

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

• Cell isolation: The MN were isolated from samples obtained by the university of Miami Brain Bank using LCM.

• Sample preparation performed using the nanoPOTS workflow. Cells are treated with 0.1% DDM (for lysis) added with DTT (protein reduction), then IAA (alkylation), then Lys-C and trypsin (protein digestion).

• Separation: Samples were injected on the column using an Ultimate 3000 RSLCnano pump. The in-line loading column is a home-packed SPE column (5cm x 75um) while the peptide separation is performed on a an in-house-packed analytical SPE column (50 cm x 30um), using a 20nL/min flow rate.

• Ionization: nanospray emmitter (2,000V)

• Mass spectrometry: Orbitrap Exploris 480. HCD fragmentation. MS1 settings: accumulation time = 200 ms; resolution = 120,000; AGC = 1E6. MS2 settings: exclusion duration = 90 s; accumulation time = 500 ms; resolution = 30,000; AGC = 1E5.

• Data analysis: Sequest HT in Proteome Discoverer (v2.5) and the search database is Swiss-Prot (July 2020).

Data collection

All data were collected from the MassIVE repository (accession ID: MSV000092119).

The sample annotations were combined from the tables in ⁠Biogen_TDP43_Round2_Reanalysis_10-13-2021_InputFiles.txt⁠ and in Groups.txt.

The PSM data were found in the ⁠Biogen_TDP43_Round2_Reanalysis_10-13-2021_PSMs.txt⁠ file. The data were converted to a QFeatures object using the scp::readSCP() function. We could not find sample annotations for MS run ID: F61, F34, F42, F88, F77, F8, F21, F5.

The peptide data were found in the ⁠Biogen_TDP43_Round2_Reanalysis_10-13-2021_PeptideGroups.txt⁠ file. The column names holding the quantitative data were adapted to match the sample names in the QFeatures object. The data were then converted to a SingleCellExperiment object and then inserted in the QFeatures object.

A similar procedure was applied to the protein data. The data were found in the ⁠Biogen_TDP43_Round2_Reanalysis_10-13-2021_Proteins.txt⁠ file. The column names were adapted, the data were converted to a SingleCellExperiment object and then inserted in the QFeatures object.

Source

All data can be downloaded from the MassIVE repository MSV000092119. The source link is: ftp://massive.ucsd.edu/v05/MSV000092119/

References

Guise, Amanda J., Santosh A. Misal, Richard Carson, Jen-Hwa Chu, Hannah Boekweg, Daisha Van Der Watt, Nora C. Welsh, et al. 2024. “TDP-43-Stratified Single-Cell Proteomics of Postmortem Human Spinal Motor Neurons Reveals Protein Dynamics in Amyotrophic Lateral Sclerosis.” Cell Reports 43 (1): 113636. (link to article).

Examples

guise2024()

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