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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Inquiry on Quantification Using b/y Ions with Zero Intensity Values #962

Open hahahahhhhahaha opened 8 months ago

hahahahhhhahaha commented 8 months ago

Dear Vadim,

Thanks for your such a great software!I am writing to seek guidance on a particular issue I've encountered while attempting to quantify proteins using b and y ions. I've noticed that each peptide seems to have only 12 b/y ions, and upon locating the intensity values for these ions, I observed that some of them have an intensity value of zero. This situation seems less than ideal for quantification purposes.

Could this issue be attributed to a potential misconfiguration in the software settings on my part? I would greatly appreciate any insights or recommendations on how to resolve this matter.

Thank you in advance for your time and assistance. I look forward to your valuable advice.

vdemichev commented 8 months ago

The PG.MaxLFQ quantity reported by DIA-NN is ready to use and is well suitable for almost all applications. What is the rationale to re-quantify proteins in this case?

Your observation about fragment ions is in line with expectations, no problem here.

hahahahhhhahaha commented 8 months ago

Thanks for your reply! And I would like to know if DIANN is able to generate information on a-ions within its feature set.