Remember RAW Meat? Man, I loved that program. Unfortunately it doesn't work for a lot of newer instruments. What if I told you that virtually every function in RAW meat is hidden in Proteome Discoverer 2.0?
They are. And they are under the plot functions.
You can plot your mass discrepancy (at PSM or peptide level), you can plot your ion injection times (for MS/MS scans or for PSMS and as a histogram or over time). You can get your charge distribution to see if that matches theoretical for your enzyme (2 or 3 for trypsin, etc.,), you can plot your missed cleavages and on and on.
Now. I picked a bad screenshot above. I can't seem to plot my TopN. Maybe I haven't found it yet. Or maybe I need to submit a feature request!
You can learn more about this here!
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