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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Visualize XIC in skyline without unimod modifications #1195

Open cutleraging opened 1 month ago

cutleraging commented 1 month ago

Hello DiaNN team,

I have been using DiaNN to analyze histone modifications. The peptides we are analyzing are first derivatized using propionic anhydride, so many of the modifications are combinations of propionyl and e.g. methyl acetyl, phospho, etc. However, these combinatorial mods are not in UNIMOD, and thus I cannot verify this data in Skyline. Moreover, when I try to use the built-in XIC viewer, I am only able to look at so many XICs at a time - I am not able to scroll down to see all of the XICs for all of the peptides I have analyzed (I also have to set the protein group to the peptide in order to visualize them).

So, is there a way to get around this so I can analyze these peptides in skyline? Or is there software to visualize the XICs from the .parquet files?

Thanks, Ronnie

vdemichev commented 1 month ago

Hi Ronnie,

I am not sure how to make it work with Skyline, I guess it might be possible if you modify the .bat file used to launch Skyline to specify the modifications, but I have little experience in that.

With the built-in Viewer, not sure if this would be helpful here, but you can select your peptide / protein group and then navigate up/down in peptide/protein list by pressing up/down arrows on the keyboard. If you work on an SSD, chromatogram loading for the new PSM should be almost instantaneous.

Finally, the .parquet files in the _xic folder can be easily read in R or Python (R arrow or Python pyarrow or polars packages). The format is quite self-explanatory, I guess should be very quick to write a script for any kind of custom plotting.

Best, Vadim