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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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slice-PASEF #1082

Open cutleraging opened 2 months ago

cutleraging commented 2 months ago

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

vdemichev commented 2 months ago

Hi Ronnie,

A general comment: Slice-PASEF data can be processed exactly the same as dia-PASEF, but also need to add —tims-scan.

  1. Same as dia-PASEF, but also add —tims-scan. Mass accuracies fixed to 15ppm.
  2. Either works.
  3. Yes, unless the library already contains properly annotated protein groups.
  4. Set them to 15ppm in the GUI.
  5. With —var-mod or —fixed-mod
  6. If you mean MBR, then yes in most cases, please see the respective section of the documentation.
  7. Yes.

Best, Vadim