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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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specify number of fragments in quantification #1025

Open hxxhust163 opened 1 month ago

hxxhust163 commented 1 month ago

Hi Vadim

Thanks for your work in DiaNN. I find that in the main out, the largest number of fragments used in quantification is 12. I mean the number of values showed in 'Fragment.Quant.Raw' column is no more than 12. I wonder if this value can be specified by the users? Or will you launch a new release with this option enabled. Thanks again!

Best wishes Xiaoxiang

vdemichev commented 1 month ago

Hi Xiaoxiang,

No, this option is not adjustable. The reason is, it's highly unlikely that fragments beyond the top 12 predicted ones could be useful for quantification.

Best, Vadim

hxxhust163 commented 4 weeks ago

Hi Vadim,

In some special cases, for example, IPF (PMID: 28604659) analysis for modified peptide, more fragments or transitions may be useful for identification or quantification. I guess it would be great if more fragments, no matter predicted or stored in a spectral library, can be considered in DiaNN. Would that be possible? Thanks a lot.

Best Xiaoxiang