feature request

support
feature request Tobias Kockmann  2018-07-11
 

Hi Panorama team,

as discussed at the skyline user meeting I would like to suggest some new features for Panorama + autoQC. I am not sure how other people use this tool, but our sample for system suitability testing contains iRT peptides. We accordingly use iRT regression as a performance measure, since the parameter estimates (slope and intercept) tell us if our LCs really deliver the commanded gradients. Unfortunately, we always have to do this offline, since Panorama does not monitor these parameters, although the skyline doc records the iRT regression on the fly. What about including diagnostic plots for RT regression in Panorama?

Another feature request: Panorama ignores the protein/peptide list context of targets. Our targets lists during autoQC runs contain a mixture of matrix peptides (BSA) and iRTs. Unfortunately, they are all displayed alike and in alphabetic order. Some sort of filtering/grouping according to peptide list/protein context would help very much! Also sorting according to hydrophobicity or iRT value would be a cool feature.

Let me know what you think about my suggestions,
Tobi

 
 
Tobias Kockmann responded:  2018-11-09

Hi Panorama Team,

hope you are doing well. Since I haven't heard anything back from you, we meanwhile implement RT~iRT regression using our own toolbox outside of the skyline & PanoramaWeb framework. :-) The following website is generated automatically

http://fgcz-ms.uzh.ch/~cpanse/autoQC01.html

every few minutes and displays the results of the model fitting for the last 24 h across our qOrbi instruments. The core code is written in R . The sample is iRT peptides in BSA digest, separated by a 20 min linear gradient. We are not using a sophisticated peak caller to find the peptide RTs, but simply rely on HR/AM and narrow XIC windows (pretty much like one would do in FreeStyle).

Greetings,
Tobi