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Published 20 hours ago • verified publisher icon vdemichev

slice-PASEF

Open cutleraging opened this issue 7 months ago • 1 comments

I am testing out the 1F slice-PASEF method from your preprint and have the following questions...

  1. I am wondering what the best practices are to run this in the DIA-NN software in terms of parameters to set?
  2. Is it better to use this with a spectral library or can it be run library-free?
  3. If I am using a spectral library, is it necessary to provide the fasta?
  4. I get this message, "Manually fix both MS1 and MS2 mass accuracies to values in range of 10-15 ppm," what does this mean?
  5. How can I specify custom PTMs, such as propionylation?
  6. Is it better to run slice-PASEF data in single- or double-pass mode?
  7. Is running slice-PASEF data compatible with ultra fast mode?

Thanks, Ronnie

cutleraging avatar Jul 05 '24 17:07 cutleraging