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Single cell proteomics and epiproteomics of cancer cells treated with a histone deacetylate inhibitor

ABSTRACT: NCI-H-358 cancer cells were treated with the histone deacetylase inhibitor mocetinostat or DMSO mock control. SIngle cells were isolated by FACs and were multiplexed using every other channel (c-Channels of the TMTPro reagent) a carrier channel of 75 control and 75 treated cells labeled with 135n were used for each experiment. Single cells were pseudo-randomized so that each following injection had an alternate mixture of control or treated cells as each label. Analysis was performed using an EvoSep system coupled to a TIMSTOF SCP. Cells were analyzed using 30SPD, 60SPD, 100SPD, 200SPD, 300SPD and 500SPD. After blank and carrier lanes, 7 cells were analyzed in each LCMS injection, allowing 210 cells, 420 cells, 700 cells, 1400 cells, 2100 cells and 3500 cells to be analyzed in a 24 hour day, respectively. Bruker .d files were converted to MGF and the reporter mass region was recalibrated to compensate for mass error. The resulting files were analyzed in Proteome Discoverer 2.4 and SCP-Viz.

INSTRUMENT(S): timsTOF fleX

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Benjamin C Orsburn

PROVIDER: MSV000093434 | MassIVE | Mon Nov 20 08:05:00 GMT 2023

SECONDARY ACCESSION(S): PXD047101

REPOSITORIES: MassIVE

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