DEqMS DIA data DIANN output

[ttessie2]

I posted a similar question on Bioconductor but it looks like this may be a better place to post.
I see in a previous question that precursors should be used in place of peptide counts regarding DIA data. If DIANN output for protein intensity is determined using MaxLFQ , is it really necessary to use the number of precursors?

[yafeng]

Hi, @ttessie2
That is true. If protein intensity estimates from single peptide (MaxLFQ), it makes no point to use the number of precursors peptide.
Since we have got several questions regarding applying DEqMS to DIA datasets, we did a systematic evaluation of DEqMS performance on multiple spike-in DIA datasets (This new manuscript is in the process of submission).

In our analysis, protein quant estimated all peptides using median sweeping performs much better compared to quantification by top3 most abundant peptides (default method in Spectronaut).

Our final recommendation is to use median sweeping to get protein quant table from peptide prepursors, and use the number of peptide precursors in DEqMS. we will update the vignettes in next release soon!

Yafeng

[MKoesters]

Hi @yafeng,

Are there any update on the manuscript or the vignette, is this already available?

Best,
Manu