I started using SIEVE about 6 months ago. And I feel like I'm finally doing label free peptide quan with grown-ups. Yes, I'm biased, but I never personally cared about lining up my chromatography (and there definitely still are reasons not to, to be elaborated on later!!)
But for plain old peptide quan, nothing beats SIEVE coupled with Proteome Discoverer right now and the two just keep getting better (more details on this, later as well!) Synergistically, you are talking about some awesome software on the way.
Anyway, I was recently asked if SIEVE could do quantitative top down data. Never thought to check, or ask! So I picked up some data files from the analysis of intact proteins dumped them in, and (BOOM!!!) quantitative data from intact proteins. So, yes, when we finally get where we're going (LC-MS/MS analysis of intact proteins) SIEVE will be ready!
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