Request to report # of quantified ions

[enonimos]

Is your feature request related to a problem? Please describe. My feature request would serve as additional value added to IonQuant outputs. This request was stimulated by discussions with @fcyu and @prvst in thread #642. The combined_protein report contains columns of Combined and Individual sample peptide/PSM counting results. As I understand, these columns are based on MSFragger and FDR validation filtering, and do not change based on IonQuant analysis, which annotates these files with intensities after FDR filtering. Since the # of identified peptides may not equal the # of quantified peptides, the latter values used by IonQuant are unknown. These values would be useful to interpret the subset of differential proteins, provide additional filtering options, or use as input to statistical frameworks (e.g., DEqMS).

Describe the solution you'd like Columns reported for quantified (razer+unique) peptides (or ions) used by IonQuant/MaxLFQ.

Describe alternatives you've considered I realize this could make the report more cumbersome as you could consider reporting for Razer, Unique, and Total Intensity quant columns. One option is to only report the values at the "Combined" level in the combined_protein report. Then, maybe a Philosopher flag can control whether individual sample quant columns are also reported? Or a different output file?

I realize that IonQuant has the "Min ions" options, so this provides an option for additional strict filtering. But this results in quant values that become 0, so I wouldn't know if that protein had a quant value at lower filter thresholds. I usually appreciate having this information for post-analysis interpretation. It would be cumbersome to generate multiple reports at different "Min ions" thresholds and then record which quant values become 0.

Additional context None