Add metric: Orbitrap injection time romeally  2023-01-17 07:30:23

Hi Panorama team,

I was wondering if it was possible to add MS1 Orbitrap injection time as a trackable metric to Panorama for Thermo data. The data are in the .raw files, so I imagine it could be extracted. This would be helpful, because if the instrument is dirty and overall instrument performance is decreasing, Orbitrap injection time may experience a compensatory increase to meet AGC limits and MS1 signal may remain relatively stable. We have seen this, where we get low protein IDs or PSMs or MS2 signal, but MS1 signal does not appear to be suffering, although injection times are high. After instrument cleaning, performance in other metrics goes up but MS1 signal does not change much and injection times return down to baseline.


jeckels responded:  2023-01-17 12:59:25

Hi Bob,

Thanks for the suggestion! This is something that we (the Skyline and Panorama development teams) discussed back in November 2022. It requires work on both the Skyline and Panorama sides.

I've logged it in the Skyline issue list here for more formal prioritization and visibility:

Do you have a specific way that you'd like to distill the injection time information? For example, track it across the whole sample, or on a per peptide/molecule basis?


Brendan MacLean responded:  2023-01-17 13:44:38

One thing that got us stalled a bit on this issue, I believe was the wide variety of methods that Skyline supports and how complex that could make this issue, especially with DIA, where you would want to track injection time on a per-window basis. It became clear that an injection time curve like what we now present for a pressure trace requires that each included spectrum used the same source of ions.

I think this post is a good reminder that we often have at least one simple set of spectra with a matching source of ions: the MS1 survey scans. These scans are frequently present across DDA, DIA, and PRM, while the MS/MS scans are quite different, and it may be that only DIA provides appropriate data for tracking injection times across sets of MS/MS scans.

Thanks for the reminder that MS1 injection time tracking still may be useful even if we haven't fully worked out when and how to make injection times for MS/MS useful.


romeally responded:  2023-01-19 13:39:09

Thanks for the responses. Our thought process was in line with Brendan's rationale: mean injection times of MS1 survey scans across the whole chromatogram could be useful to track. For example, a consistent change from several milliseconds before instrument cleaning to sub-millisecond after cleaning could be a sign that transmission was improved and performance is back to baseline. Obviously, there will be variation across the chromatogram as the sampling population of precursors change, so perhaps even the SD/variance of MS1 injection time would have some utility. I'm sure there are unforeseen complications in implementing this, but right now we are just scrolling through scan headers in freestyle to get an idea of what is going on with the injection times, which is hardly a systematic view of the whole run.