lpsTimecourse_mulvey2021 | R Documentation |
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.
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)
These data are instances of class MSnSet
from package
MSnbase
.
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.
The data was generated by C. Mulvey at the Cambridge Centre for Proteomics. http://www.bio.cam.ac.uk/proteomics/.
data(lpsTimecourse_mulvey2021)
lpsTimecourse_mulvey2021
pData(lpsTimecourse_mulvey2021)
head(exprs(lpsTimecourse_mulvey2021))
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