Issue 612: Support Pressure Traces in Skyline .skyd files

issues
Status:open
Assigned To:Nick Shulman
Type:Todo
Area:Skyline
Priority:2
Milestone:4.2
Opened:2018-11-23 by Brendan MacLean
Changed:2019-05-08 by matt.chambers42
Resolved:
Resolution:
Closed:
2018-11-23 Brendan MacLean
Title»Improve global chromatograms (TIC, BPC and Pressure Traces) in Skyline .skyd files
Assigned ToGuest»matt.chambers42@gmail.com
Type»Todo
Area»Skyline
Priority»2
Milestone»4.2
Currently, we have two "global chromatograms" (TIC and BPC) which we store in the SKYD files of runs extracted from full-scan files which include MS1 scans. The MS1 scans are required and both chromatograms are calculated based on those spectra, regardless of whether we could get them directly from ProteoWizard.

I would like to switch to getting them from ProteoWizard when we can, as this likely has real performance benefits. Also, we should be getting at least the TIC from ProteoWizard in SRM data, since it always seems to be present, and we just skip over it, as we have since the early days of Skyline, before I implemented this function for Skyline full-scan data.

For a while, Brian Pratt short-circuited our extraction code to skip spectra before and after we had anything scheduled for extraction, and the benefit was clear in the MS1 tutorial test. Getting TIC and BPC directly might allow us to get back to that when they are present.

One thing I am not sure about is whether we are storing scan IDs for these chromatograms and switching to ProteoWizard chromatograms might disable the ability to click on these chromatograms and see the underlying spectra. I am not sure this is a big deal, but something to consider. We don't care about mass error (the other benefit of extraction from spectra) for these chromatograms, because they have not target m/z values.

Finally, I would like to have Pressure Traces written to SKYD files as a third global chromatogram (time, intensity pairs), because SCIEX and SCIEX users have expressed interest in seeing this information in PanoramaQC. Passing this information through the Skyline SKYD file seems like the easiest way to do this and it would allow these users to view the information in Skyline also. Is this available for other vendors? I have only ever heard it requested for SCIEX instruments, but it seems like a chromatography thing. (Okay to separate this into two issues, if you prefer)

2018-12-06 matt.chambers42
Almost all vendors have TIC chromatograms for all acquisition modes. IIRC Sciex is the only one that has the BP chromatogram. However, it's a per-wiff-experiment thing and we have to merge them on the pwiz side to get a per-run chromatogram. If you can give up the BPC, then for almost all vendors you can get your run-level chromatograms very quickly. If you can't give up BPC, then only Sciex is really going to benefit from this effort, right? If you want I can put together a more detailed table of what vendors provide TIC and/or BPC and/or chromatography status info. Several other vendors have chromatography status info, depending on the MS/pump/firmware combination. I doubt even Sciex has pressure trace in all of its WIFF files.

2019-01-15 Brendan MacLean
TitleImprove global chromatograms (TIC, BPC and Pressure Traces) in Skyline .skyd files»Support Pressure Traces in Skyline .skyd files
Notify»christie.hunter
Let's hold off on TIC and BPC and just focus on the pressure traces.

Adding Christie Hunter who was interested in this feature at ASMS last year. Christie, will this information be available in all WIFF files?

ProCAN also expressed interest in having pressure traces as part of AutoQC.

2019-01-21 Brendan MacLean
Notifychristie.hunter»christie.hunter;Josh Eckels
From Christie:

Hi there,
So for *.wiff files where the LC was a SCIEX low flow system it will always have pressure. But if other LC systems are used, it may or may not record the pressure trace into the wiff… I will also dig in to see if the ExionLC write out pressure traces into wiffs… That is the other major LC that we would see with wiff files.

ProCan uses all SCIEX LCs so that should be no problem for them!

I would have to follow up with wiff2 files to understand the road map for pressure traces in that file format.

Christie

2019-04-04 matt.chambers42
Hi Brendan,

Out of 84 assorted WIFF files that I have sitting around for testing purposes, only 6 have pressure traces. In these cases, pressure is always the first channel, and pressure always appears in the channel name, but 6 is an awfully small set to make a heuristic with. One file has both loading pump pressure and gradient column pressure: which one is desired?

50uMpyrone-8uL-01 (channel 1, Agilent Pump - Agilent Pump Pressure (0))
GlycyrrMRM-Blank (channel 1, AAO Companion App. - Pump_Pressure)
GlycyrrMRM-Blank (channel 2, AAO Companion App. - UV_VIS_1)
GlycyrrMRM-Blank (channel 3, AAO Companion App. - UV_VIS_2)
HLAI-ACD 023 NewMethod2 Inj4 (channel 1, AAO Companion App. - MicroPump_Pressure)
Hoofnagle_01_IDA (channel 1, AAO Companion App. - Loading Pump Column Pressure)
Hoofnagle_01_IDA (channel 2, AAO Companion App. - Loading Pump Pump A Flowrate)
Hoofnagle_01_IDA (channel 3, AAO Companion App. - Loading Pump Pump B Flowrate)
Hoofnagle_01_IDA (channel 4, AAO Companion App. - Gradient 1 Column Pressure)
Hoofnagle_01_IDA (channel 5, AAO Companion App. - Gradient 1 Pump A Flowrate)
Hoofnagle_01_IDA (channel 6, AAO Companion App. - Gradient 1 Pump B Flowrate)
KIT1-30-3_105905_01_0_1_1_01_10000001 (channel 1, Agilent Pump - Agilent Pump Pressure (0))
RMMS11b (channel 1, Capillary Pump - Pressure)
RMMS11b (channel 2, Capillary Pump - Flow)
RMMS11b (channel 3, Capillary Pump - B)

The Agilent MIDAC and MHDAC APIs don't have a way that I can see to get pump pressure, but many other MS-specific variables are available. Some of my example files do have files like QuatPump1 and NanoPump1 with cd and cg extensions which appear to be metadata and array files in some binary format. It probably wouldn't be too hard to read these arrays, but it would be rather hacky.

Thermo RAW files often have the LCD pump/autosampler methods embedded in them, and like Agilent have many MS-specific variables available in the "Status Log", but I don't see a way to get pump pressure.

Waters RAW has MS-specific variables stored for each scan time, but no pump pressure as far as I can tell.

Shimadzu QTOF has neither MS-specific variables or pump pressure as far as I can tell.

The most recent Bruker TIMS data Stephanie sent us has chromatography-data.sqlite files which contain pump pressure. Actually 2. What to do with A and B pressures?
Flowsensor A Flow
Pump A Pressure
Pump A Speed
Pump A Temperature
Pump A Volume
Valve A Angle
Solvent B Composition
Flowsensor B Flow
Pump B Pressure
Pump B Speed
Pump B Temperature
Pump B Volume
Valve B Angle
Column Temperature
Valve I Angle
Valve T Angle
Sample Tray Temperature

So, assuming we go forward with just Sciex and Bruker pressure traces, shall I use the simple heuristic of taking traces which have "pump" and "pressure" in the name? What to do when there are multiple matches (e.g. Pump A and B pressure)?

2019-04-08 Brendan MacLean
Matt, can you check out the CPTAC Study 9s and 9 data sets? I know a fair number of SCIEX instruments were used and I remember that pressure traces were an important topic of the system suitability discussion at the first CPTAC instrument operators meeting at The Broad Institute.

https://panoramaweb.org/study_9s.url

19    WIFF
20    RAW-Thermo
32    WIFF
52    WIFF
54    WIFF
56    WIFF
56A    WIFF
56B    d-Agilent
65    RAW-Thermo
73    WIFF
86    WIFF
86A    raw-Waters
90    d-Agilent
95    WIFF
95    WIFF
98    WIFF

https://panoramaweb.org/cptac_study9.url

19    WIFF
32    WIFF
52    WIFF
54    WIFF
56A    WIFF
56B    d-Agilent
56C    raw-Waters
65    RAW-Thermo
73    WIFF
73A    raw-Waters
86    WIFF
86A    raw-Waters
90    d-Agilent

2019-04-09 matt.chambers42
I was able to download raw data for study 9s but not 9 - I don't see the raw data tab for that, only Panorama Dashboard and Data Pipeline.

For the 22 wiff files in study 9s, only 2 have traces:
Site95_031109_Study9S_Cond-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 1, AAO Companion App. - MicroPump_MasterPressure)
Site95_031109_Study9S_Cond-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 2, AAO Companion App. - LoadingPump_Pressure)
Site95_031109_Study9S_Cond-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 3, AAO Companion App. - ColumnOven_Temp)
Site95_031109_Study9S_Cond-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 4, AAO Companion App. - ColumnPressure)
Site95_031109_Study9S_Cond-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 5, AAO Companion App. - ColumnOven_FC_BridgeFlow)
Site95_031109_Study9S_Cond-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 6, AAO Companion App. - ColumnOven_FC_Stepper)

Site95_041109_Study9S_PHASE-I-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 1, AAO Companion App. - MicroPump_MasterPressure)
Site95_041109_Study9S_PHASE-I-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 2, AAO Companion App. - LoadingPump_Pressure)
Site95_041109_Study9S_PHASE-I-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 3, AAO Companion App. - ColumnOven_Temp)
Site95_041109_Study9S_PHASE-I-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 4, AAO Companion App. - ColumnPressure)
Site95_041109_Study9S_PHASE-I-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 5, AAO Companion App. - ColumnOven_FC_BridgeFlow)
Site95_041109_Study9S_PHASE-I-Site95_STUDY9S_PHASEI_6ProtMix_QC_01 (channel 6, AAO Companion App. - ColumnOven_FC_Stepper)

Not encouraging?

2019-04-09 Brendan MacLean
Notifychristie.hunter;Josh Eckels»christie.hunter;Josh Eckels;Susan Abbatiello;birgitxschilling
Adding Sue Abbatiello and Birgit Schilling. Yeah, you reminded me that the Study 9 raw data never got put up. Surprising that Study 9S had so few pressure traces. I remember seeing them talk about these during the CPTAC instrument operators meeting that kicked off CPTAC use of Skyline.

2019-04-13 Brendan MacLean
Notifychristie.hunter;Josh Eckels;Susan Abbatiello;birgitxschilling»christie.hunter;Josh Eckels;Susan Abbatiello;birgitxschilling;Paul Auger;kristin geddes
Christie has also agreed to provide example data, and Sue says there is a configuration step required to get these pressure traces included in the WIFF files.

We are expecting to use this with AutoQC where we can simply require users to make this configuration adjustment in order to get this feature. So, not a huge deal if it is not yet very common. As long as it is possible and we can get enough data to test the implementation, we can get started.

Now also adding Paul Auger and Kristin Geddes who may have access to SCIEX instruments where they can get us WIFF files with pressure traces for their AutoQC runs, and if they are not already storing the pressure traces in those WIFF files, they can look into how much work it would be to change that and start getting us WIFF files with this information in a system suitability setting.

2019-05-08 matt.chambers42
Assigned Tomatt.chambers42@gmail.com»Nick Shulman
Notifychristie.hunter;Josh Eckels;Susan Abbatiello;birgitxschilling;Paul Auger;kristin geddes»christie.hunter;Josh Eckels;Susan Abbatiello;birgitxschilling;Paul Auger;kristin geddes;matt.chambers42