More parameters for MSstats

### 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 https://github.com/bigbio/quantms/issues/282 https://github.com/bigbio/quantms/blob/a860ade5d655f9d50b7dbebaad71f3da83243b7d/bin/msstats_tmt.R#L817
- [ ] 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

_No response_

### System information

_No response_