Reviewer 1: FAIR principles concern

[ypriverol]

The topic of interoperability seems nearly entirely absent in the manuscript. A text search for “interop” yields only 3 hits and 2 are just the definition of FAIR, and then last just an offhand remark. It would seem that interoperability is key topic that should be addressed in the manuscript. Should proteomics software support standards? Are ad-hoc TSV or JSON formats okay/good/better? I am startled to find no mention of the PSI or mzML or any such attempts (useful or not) to provide data formats, guidelines, and other standards whose stated goal is to enable interoperability of software. How common is the thought “well, this newly published software tool seems nice, but it does not interoperate with the input/output of my toolchain, so what value is it?” How can the field make progress with that problem? I think the manuscript should be enhanced to address this aspect.

I will take care of this. @ypriverol