More parameters for MSstats

[ypriverol]

Description of the bug

For MSstats would be good to have more parametrization:

• MSstats has multiple performance issues that can be tackle using parameters.
  • TMT plots for QC and ProfilePlot. When using in the parameters the option allonly the plots are summary, if the parameter has the option all, then it prints the plot for every protein which is memory consuming, see error Another quantms MSstats error #282

    quantms/bin/msstats_tmt.R

    Line 817 in a860ade

    dataProcessPlotsTMT(processed.quant, "ProfilePlot", width=12, height=12, which.Protein="allonly")

  • In the TMT and LFQ when too many proteins or peptides are reported, it doesn't matter how much memory is allocated the MSstats analysis fail. Some parameters that can improve performance on MSstats are: https://groups.google.com/g/msstats/c/bjbzYRqmldc

Command used and terminal output

No response

Relevant files

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System information

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