ProteoMS: Quality Control of Protemics Data

Description Usage Arguments Value Examples

Acquisition Cycle and MS/MS

1	PlotAcquisitionCycle(MQCombined, palette = "Set2", plots_per_page = 5)

`MQCombined`	Object list containing all the files from the MaxQuant output. It is the result from using `make_MQCombined`.
`palette`	The palette from the Package RColorBrewer. By default is 'Set2'.
`plots_per_page`	Establish the maximum number of plots per page.

Two plots per sample, one with the cycle tyme vs retention time, and MS/MS count vs retention time.

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MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics")
MQCombined <- make_MQCombined(MQPathCombined)
PlotAcquisitionCycle(MQCombined)