Optimization of injection or fill time in Exploris 240

Optimization of injection or fill time in Exploris 240 danielacgranato  2022-05-16

We are performing PRM in Exploris 240 and we would like to optimize the best injection time/fill time for each peptide, especially in the case of peptides that compete in the same scheduled window. Can this optimization be performed in Skyline? Can Skyline extract information of best injection time or acquisition time? Can Skyline help us evaluate what peptides need to improve injection time?

Thank you very much.
Best, Daniela

Mike MacCoss responded:  2022-05-16

Hi Daniela,
This is not currently something that we do within Skyline. The measurement is whether each peptide is underfilling the Orbitrap or not. Within our lab, most of these analyses are done outside of Skyline. The injection time is obviously per each spectrum but in generating an extracted ion chromatogram we collect that data from many spectra. Do you have suggestions for how you might want this information displayed? We've made plots like this before https://pubmed.ncbi.nlm.nih.gov/32867497/#&gid=article-figures&pid=figure-6-uid-5 but it isn't clear to me how this would fit into the Skyline UI. Also, it would only be a plot that would be relevant for Thermo ion trap mass spectrometers.

We've also discussed tracking injection time for a specific peptide as part of the system suitability process in AutoQC (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5406750/). This seems like an easier thing to track and report but even then it isn't clear whether we should be tracking best injection time, average injection time, total ions, etc... for each peak.

It would be great to hear thoughts or examples of plots that you might find helpful. We spend a lot of time thinking about injection time and the ion population in our experiments but we don't know of the best way to report this in a general way.