Protein ID in new version of MaxQaunt

[Low Teck Yew]

Dear all,

I am trying to reanalyze of of my old data acquired with Triple TOF 5600 many years ago. I realized that the number of peptides and proteins groups drastically reduced when the new version of MQ is used. A number of new parameter are available under INSTRUMENT. In the past, I used to choose 50 ppm for MS1 tolerance and 0.1 Da for MS2 tolerance; and may be going to top 10 msms peaks per 100 Da bin. I am wondering if someone can provide a handbook about choosing those new parameters? Especially those DIA ones.

Thank you.

[Inês Caramelo]

Hello, 

I have never used a previous version but my data from TOF 6600 is getting a really low sequence coverage, comparing to Protein Pilote.