Pressure output?

Pressure output? alejandro.cohen  2020-02-20 09:43

Hi Skyline people,

I work with an Agilent 1290 coupled to a Qtrap5500 running MRM metabolomics which I analyze using Skyline (.dam methods, .wiff datafiles). Analyst is recording the column pressure output signals, however viewing these using Analyst is cumbersome and time intensive when working with big sample batches. We have encountered erratic behaviour of our chromatography, accompanied by unusual pressure profiles for samples, which tend to correct themselves after a few runs.

As part of our QC, it would be great if skyline would be able to add (overlap) the pressure traces on each chromatogram. Is this possible? I know each vendor 'hides' the pressure traces in different output and channels... but the information is there :)

I know this request has been done in the past... here another kind 'reminder'



Alejandro Cohen, Ph.D.

Scientific Director
Biological Mass Spectrometry Core Facility. Room N-105
Life Sciences Research Institute

Brian Pratt responded:  2020-02-20 10:15

Hi Alex,

We've done some work in that area recently. You should be able to select the QC traces under the Transitions menu (see attached graphic) as long as the channel names have "Pressure" or "Flow" in the name. You can easily switch between QC traces for each sample. But you won't be able to overlay the chromatograms with the traces, unfortunately (we welcome feedback, if that's not quite what you'd hoped for).

Since you're doing MRM, you could actually do the overlay with SeeMS. But with SeeMS it's not as convenient to switch between the same trace for different samples.

Thanks for using the Skyline support board,

Brian Pratt

alejandro.cohen responded:  2020-02-20 11:04


That's great! hope you can work on an overlay option if that is possible!



Brian Pratt responded:  2020-02-20 11:20

Hi Alex,

Can you describe what your dream display would be, given that the there would be two or more distinct sets of units? Would a unitless display of the QC traces suffice when overlaid on the chromatograms?

Thanks for helping improve Skyline!


alejandro.cohen responded:  2020-02-20 11:44


Yes, a UNIT-less display of the pressure traces on the chromatograms would be nice.

-Have a maximum pressure replicate comparison to monitor health of column.
-Being able of overlay pressure traces between different samples on the same plot (just for publication purpsoses). This would actually be nice not only for the pressure plots, but also for the intensity signals for the targets (other programs allow you to slightly offset X (intensity) and Y (time) among different samples to illustrate 'biological differences'. I realize this would probably be another separate request.

Chris Ashwood responded:  2020-04-21 07:33

Sorry to jump in here, Brian and Alejandro, but is this option also available for Thermo raw files?
I'm using Skyline daily with a raw file that has pressure as NCap_Pump_Pressure but there is no QC option under the transitions drop down box.

I have uploaded a complete Skyline assay under the name Pressure_check2.


alejandro.cohen responded:  2020-04-21 07:45

Hi Chris,

I believe it can be done, however, I'm working from home and I dont have immediate access to my QE raw files. I'll let Brian weigh in.



Brian Pratt responded:  2020-04-21 10:13

Unfortunately we don't yet have a way to reliably read that out of most vendor raw files. It's often not in there at all, or when it is there it's stored in a catch-all manner and labeled ad hoc (might be pressure, might be a UV detector, etc).

If anyone has examples (for any mass spec vendor) where they feel it should be pretty easy for Skyline to reliably find QC traces we'd love to seem them.


Chris Ashwood responded:  2020-04-21 14:29

The MSFilereader 3.0 documentation for Thermo appears to have a possible solution:

The GetChroData function can be used to pull out chromatograms using the following function:
longGetChroData(long nChroType1, long nChroOperator, long nChroType2, LPCTSTR szFilter, LPCTSTR szMassRanges1, LPCTSTR szMassRanges2, double dDelay, double FAR* pdStartTime,double FAR* pdEndTime, long nSmoothingType, long nSmoothingValue, VARIANT FAR* pvarChroData, VARIANT FAR* pvarPeakFlags, long FAR* pnArraySize)

To get the analog 1 chromatographic trace, a quick example could be:
longGetChroData (long Analog 1 (0), 0 , Analog 1 (0), NULL, NULL, 0.0, 0, 0, 0)

I don't know if chromatograms are extracted from raw files with MSFileReader with Skyline already so I'm going to assume that this will require significant effort. Also, it looks like you can't pull the name of the channel so the labels at best would appear as Analog 1, Analog 2 etc instead of the descriptors we use. As the analog channels can be configured differently (e.g. analog 1 = column pressure on one system and analog 2 = column pressure on another), this might not be feasible for wide benefit.


Brian Pratt responded:  2020-04-22 09:10

I suppose we could just naively display whatever chromatograms we can find, rather than trying to identify them - displaying "analog1" etc might be better than nothing, but could also be pretty confusing?


mtodenki responded:  2023-07-26 10:52

Hello Skyline team,

I was hoping to get information regarding the ability to display pressure outputs from Waters data files? Similarly to Chris, I also do not see an ability to add pressure traces under transitions. Would it be possible to monitor pressure overtime in AutoQC?

Thank you for your time,

Melanie Odenkirk
Research Scientist, Jessica Prenni Laboratory, Colorado State University
Periodic Table of Food Initiative

Nick Shulman responded:  2023-07-30 16:12
Melanie Odenkirk,

When I look at the ProteoWizard source code, it appears that the only types of files which have any of these pressure trace or flow rate chromatograms are Agilent, Sciex and Thermo.
I do not think that Skyline can display any pressure traces from Waters data.
-- Nick