zhu2018MCP: Zhu et al. 2018 (Mol. Cel. Prot.): rat brain laser...

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

Zhu et al. 2018 (Mol. Cel. Prot.): rat brain laser dissections

Description

Near single-cell proteomics data of laser captured micro-dissection samples. The samples are 24 brain sections from rat pups (day 17). The slices are 12 um thick squares of either 50, 100, or 200 um width. 5 samples were dissected from the corpus callum (CC), 4 samples were dissected from the corpus collosum (CP), 13 samples were extracted from the cerebral cortex (CTX), and 2 samples are labeled as (Mix).

Usage

zhu2018MCP

Format

A QFeatures object with 4 assays, each assay being a SingleCellExperiment object:

• peptides: quantitative information for 13,055 peptides from 24 samples

• proteins_intensity: protein intensities for 2,257 proteins from 24 samples

• proteins_LFQ: LFQ intensities for 2,257 proteins from 24 samples

• proteins_iBAQ: iBAQ values for 2,257 proteins from 24 samples

Sample annotation is stored in colData(zhu2018MCP()).

Acquisition protocol

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

• Cell isolation: brain patches were collected using laser-capture microdissection (PALM MicroBeam) on flash frozen rat (Rattus norvergicus) brain tissues. Note that the samples were stained with H&E before dissection for histological analysis. DMSO is used as sample collection solution

• Sample preparation performed using the nanoPOTs device: DMSO evaporation + protein extraction (DMM + DTT) + alkylation (IAA)

  • Lys-C digestion + trypsin digestion.

• Separation: nanoLC (Dionex UltiMate with an in-house packed 60cm x 30um LC columns; 50nL/min)

• Ionization: ESI (2,000V)

• Mass spectrometry: Thermo Fisher Orbitrap Fusion Lumos Tribrid (MS1 accumulation time = 246ms; MS1 resolution = 120,000; MS1 AGC = 3E6). The MS/MS settings depend on the sample size, excepted for the AGC = 1E5. 50um (time = 502ms; resolution = 240,000), 100um (time = 246ms; resolution = 120,000), 200um (time = 118ms; resolution = 60,000).

• Data analysis: MaxQuant (v1.5.3.30) + Perseus (v1.5.6.0) + Origin Pro 2017

Data collection

The data were collected from the PRIDE repository (accession ID: PXD008844). We downloaded the MaxQuant_Peptides.txt and the MaxQuant_ProteinGroups.txt files containing the combined identification and quantification results. The sample annotations were inferred from the names of columns holding the quantification data and the information in the article. The peptides data were converted to a SingleCellExperiment object. We split the protein table to separate the three types of quantification: protein intensity, label-free quantitification (LFQ) and intensity based absolute quantification (iBAQ). Each table is converted to a SingleCellExperiment object along with the remaining protein annotations. The 4 objects are combined in a single QFeatures object and feature links are created based on the peptide leading razor protein ID and the protein ID.

Source

The PSM data can be downloaded from the PRIDE repository PXD008844. FTP link ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/07/PXD008844

References

Zhu, Ying, Maowei Dou, Paul D. Piehowski, Yiran Liang, Fangjun Wang, Rosalie K. Chu, William B. Chrisler, et al. 2018. “Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets.” Molecular & Cellular Proteomics: MCP 17 (9): 1864–74 (link to article).

Examples

zhu2018MCP()

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