Thanks to everyone who contributed. The answer is largely "no", although there have been some efforts on the TF side. There is also a concern about the QA/QC involved in creating TF & E3 specificity lists, although that sort of concern is pretty common (& justifiable) in any high-throughput effort.

The latter.

Much in the spirit of Smith's "i, Robot".

METAPs may require a name change, given the experimental observation of its willingness to remove a leucine when it happens to be at the start of translation. #proteomics

I do not accept the delineation of “predatory” journals when these for profits are not considered predatory simply because of prestige. And yeah, system has been broke for quite a while and now is just accelerating. One day scientists will realize what “publishing” means and doesn’t mean. I hope.

Particularly when the 'most prestigious' journals have their share of problematic publications & retractions but try to hide or delay a call on those in every manner imaginable.
Then again, the publishing system is also reflecting how broken our university & funding systems are.

The guy mentioned had 45 retraction, all on the same journal (Science of the Total Environment) before someone said, "Well, there is something wrong here." Academy and founding agencies reward this hyperprolific behavior. Mass spec field is not an exception.

Goes without saying, but when are we expecting to see routine proteoform annotation included with this type of information?

What I don't know is how noisy this sort of information is in practice. In many areas (e.g., PPI information) the push tends to be for larger & larger lists, which ironically means that they become less useful for any sort of predictive application. Are TF-target lists immune to this pressure?

The entire scientific publishing world has made nothing but wrong turns since the old regime of printing magazines & mailing them out on a regular basis became obsolete.

That does sound interesting: I will take a look.

If you are talking about this sort of thing (pmc.ncbi.nlm.nih.gov/articles/PMC...), yes that is at least in the ball park on the translation rate end of things. Factors affecting changes in protein lifetime aren't part of the scheme, so it doesn't really fill the whole bill by any means.

That would be a reasonable analogy. Something that would allow you to take a pattern of protein concentration changes and propose sets of transcription factors and E3 ligases that would account for the changes. Sources & sinks.

These parties also support a type of broken Capitalism of the sort that Adam Smith condemned back in 1776: a very visible hand skewing markets & choosing winners based on personal relationships. Unfortunately their opposition also support these things, only wearing a different coloured hat.