thpTimecourse2021: Protein and PMS-level datasets from temporal abundance...

In lgatto/pRolocdata: Data accompanying the pRoloc package

Protein and PMS-level datasets from temporal abundance profiling experiments of THP-1 human leukaema cells stimulated with LPS

Description

These are timecourse proteomics datasets output from temporal abundance experiments on THP-1 human leukaema cells stimulated with LPS at 0, 2, 4, 6, 12 and 24 hours.

Usage

data(lpsTimecourse_mulvey2021)
data(lpsTimecourse_rep1_mulvey2021)
data(lpsTimecourse_rep2_mulvey2021)
data(lpsTimecourse_rep3_mulvey2021)
data(psms_lpsTimecourse_rep1_mulvey2021)
data(psms_lpsTimecourse_rep2_mulvey2021)
data(psms_lpsTimecourse_rep3_mulvey2021)

Format

These data are instances of class MSnSet from package MSnbase.

Details

These are triplicate timecourse proteomics datasets output from temporal abundance experiments on THP-1 human leukaema cells stimulated with LPS. THP-1 total cell lysates were harvested at specific time-points of LPS stimulation; 0, 2, 4, 6, 12 and 24 hours. These were then digested, labelled with TMT 6plex, and analysed by LC-MS/MS on the Q-Exactive MS (Thermo). The resulting datasets were processed by Proteome Discoverer software (v2.1, Thermo) and imported and analysed in R using the packages MSnbase and pRoloc.

PSM-level and protein-level csv files are available in the codeextdata directory and have been imported as MSnSet instances using readMSnSet2. There are 3 replicates and the PSM-level and protein-level datasets are denoted accordingly.

The dataset lpsTimecourse_mulvey2021 contains the triplicates concatenated thus including only proteins common across all experiments, and is that which was used in the core analayis in the manuscipt by Mulvey et al 2021. The featureData columns contain the output (adjusted) p-values output from the temporal abundance analysis that was performed using limma and as described in Mulvey et al 2021.

Source

The data was generated by C. Mulvey at the Cambridge Centre for Proteomics. http://www.bio.cam.ac.uk/proteomics/.

Examples

data(lpsTimecourse_mulvey2021)
lpsTimecourse_mulvey2021
pData(lpsTimecourse_mulvey2021)
head(exprs(lpsTimecourse_mulvey2021))

lgatto/pRolocdata documentation built on April 7, 2023, 1:56 a.m.