The quantitative value of peptide information for a specific protein is inconsistent with the abundance value of the protein LFQ value

[xinxin-web]

Hello, regarding my 6 proteomics samples, which are divided into control group and knockout group, my western blot results show that they have been successfully knocked out, but when I searched the library using DIA.NN.1.8.1 version, I found that in the peptide quantitative information, the control group of this protein has more precursors and the knockout group has fewer. This is in line with our expected results, but this difference is not reflected in the protein quantitative information

[vdemichev]

Hi,

Quant was much improved in DIA-NN 1.9.2, I recommend using it.
If you'd like run-specific protein confidence, also please use the main report and filter it based on PG.Q.Value, then the false hits should just disappear.

Best,
Vadim

[xinxin-web]

Thank you for your sincere reply. When using PG.Q.Value for filtering, what value will Q.value generally use for filtering? Best wishes xinxin

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On Thu, Jan 2, 2025 at 5:58 PM Vadim Demichev ***@***.***> wrote: Hi, Quant was much improved in DIA-NN 1.9.2, I recommend using it. If you'd like run-specific protein confidence, also please use the main report and filter it based on PG.Q.Value, then the false hits should just disappear. Best, Vadim — Reply to this email directly, view it on GitHub <#1324 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJZ7QSSWBLWIFZ3Z2VTY44L2IUESZAVCNFSM6AAAAABUPSAK6GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNRXGUYTSMRZGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[vdemichev]

Usually 0.01. You can also filter based on PG.PEP, gives you more confidence.

[xinxin-web]

Thank you very much for your reply, I will try the two methods you mentioned.
Best wishes