quantifying phosphopeptides/sites

[sooheon]

Could directLFQ be adjusted to output phosphopeptide/site level aggregations?

I'm curious how much effort this would take.

[ammarcsj]

Hi, if you put in a table that looks somewhat like the one below, it will also work for site level aggregations. So in the 'protein' column, you can put the collapsed ptmsite_ID and in the 'ion' column you can put all the precursors that map to the site. You can simply run directLFQ on this table:

lfq_manager.run_lfq(input_file, input_type_to_use = "directlfq").

Let me know if you have further questions

[sooheon]

Sorry the notation inside your protein / ion columns is a little unfamiliar to me — what would be the equivalent columns from DIA-NN report.parquet or tsv?

[ammarcsj]

could you share a small snippet of the .tsv file here? Then I could have a look

[sooheon]

Thank you that'd be very helpful. This is report.parquet:

https://pastebin.com/raw/hf72a22j

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[ammarcsj]

Thanks, however, I would need it with headers and also all available columns. You have searched with phosphorylation?

[sooheon]

My bad, didn't check columns. Yes, you can see in Modified.Sequence output that UniMod:21 is included.

https://pastebin.com/vPmHgpz0

[ammarcsj]

Thanks! From what I can see, you can use the Precursor.Id as "ion" column and the Protein.Sites as "protein" column and then reformat the table. Additional filters might be necessary, e.g. PTM.Q.Value or PTM.Site.Confidence. Best check the DIA-NN manual for that.

[sooheon]

Thank you. Is there any special notation for one observed peptide with multiple modifications, or are they just treated as a single unit?

[ammarcsj]

I believe that this will be accounted for in the Protein.Sites column, in your example, there is eg listed: Q96JP5:S69. Let's assume there would be another modified site closeby, then this would probably be something like Q96JP5:S69:Y71. Maybe you can check your table for such examples.