Feature request: Add retention time information to ion.tsv table

[hollenstein]

Dear FragPipe Team,

Is your feature request related to a problem? The request is not directly related to a problem but it would allow using the FragPipe outputs for additional workflows / use cases. Here are some examples.

In the daily operations of our MS facility, we sometimes need to manually validate the identification or quantification of a particular PTM or protein. To do so it is often helpful to be able to look up the retention time (that was used by the software) of a particular ion (LC-MS feature).

Since FragPipe is quite fast compared to other pipelines, it is also a good choice for QC applications. Here it would be useful to have information regarding retention time apex and FWHM (or retention span), in order to monitor LC performance.

There are retention time prediction tools, for example for generating time-scheduled PRM target lists, that allow calibrating the RT prediction with previous LC-MS data from your system. Having an ion table with the peak retention time would make it straight forward to use the FragPipe output for this calibration.

Describe the solution you'd like Adding retention time columns to the ion.tsv table. I think it would be most useful to have a peak retention time column and something like a start/end time or FWHM column.

I think it is not necessary to have this information in the combined_ion.tsv table, as it is quite simple to either concatenate all ion.tsv tables, or create a pivoted table from them, containing the retention time columns.

Thanks for your consideration, David