Protein ID in new version of MaxQaunt

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Low Teck Yew

Apr 1, 2021, 1:13:02 PM4/1/21
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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

Nov 11, 2021, 5:16:19 AM11/11/21
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I have never used a previous version but my data from TOF 6600 is getting a really low sequence coverage, comparing to Protein Pilote.

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