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Wang-kaifei / DBReducer

A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics
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Quick question about configuration setting #2

Closed progistar closed 5 months ago

progistar commented 6 months ago

Hi,

I have a quick question about configuration setting in DBReducer.cfg

1) What kinds of activation_type supported? (e.g., HCD-FTMS) 2) Does it support non-enzymatic condition? 3) What does "msmsnum=32" mean?

Thanks in advance!

Wang-kaifei commented 6 months ago

Hi,

  1. The "activation_type" means the type of mass spectrometry data. HCD-FTMS, HCD-ITMS, CID-FTMS and CID-ITMS are supported.
  2. In fact, the default of DBReducer is non-specific digestion with Trypsin. This is basically no different from non-enzymatic condition. If you need other specific enzyme digestion types, I can provide a new version later.
  3. "msmsnum=" means the number of files for the input dataset.

Feel free to contact me if you have any questions!

progistar commented 6 months ago

Thank you for your quick reply. I am confused the meaning of "non-specific digestion with Trypsin." It would be grateful if you could give me more specific explanation.

Wang-kaifei commented 5 months ago

Sorry for the confusion. "Non-specific digestion" means that the protein is allowed to be cleaved at any site. Specifically, although trypsin is set, enzymatic cleavage at non-KR amino acids is allowed.

progistar commented 5 months ago

I appreciate to your kind reply. It helps me!