Skip to main content
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index] [List Home]
Re: [chemclipse-dev] Which data model can store the raw data from TOF mass spectrometer?
Hi Philip,

I think I can store the calculated Ion in one ScanMSD, but first I must find a place to store my raw data from acquisition card of TOF mass spectrameter. The raw data is a serie of time(in nanoseconds) - intensity. ChromatographMSC can only store ScanMSD, not time-intensity serie.


Best regards,

Trig

2016-07-01 20:45 GMT+08:00 Philip Wenig <philip.wenig@xxxxxxxxxxxxx>:
Trig,

yep, OpenChrom supports various detector types. You are right, the CSD types stores the TIC signal only as e.g. a FID captures the current.

CSD = Current Selective Detectors (FID, ECD, NPD, ...)
MSD = Mass Selective Detectors (Quadrupole, IonTrap, TandenMS, OrbiTrap, TOF, ...)
WSD = Wavelength Selective Detectors (DAD, UV/Vis, ...)

So you can use the MSD scan type, e.g.:

IVendorScan scan = new VendorScan();
scan.setRetentionTime(500); // currently milliseconds
scan.setMassSpectrometer((short)2); // 1 = MS1, 2 = MS2
scan.setMassSpectrumType((short)1); // centroid = 0, profile = ""> //
scan.addIon(new Ion(104.18983d, 2506.0f));
scan.addIon(new Ion(104.283d, 506.0f));
scan.addIon(new Ion(104.3049d, 6.0f));
scan.addIon(new Ion(104.384984d, 29206.0f));
...

OpenChrom offers several way to display the data. It could be either nominal, high resolution, centroid or profile mode, see attached screenshot.


Best,
Philip


Am 01.07.2016 um 08:39 schrieb Trig Chen:
Regardless of the unit of time, the ScanCSD model stores retention time and total signal data, seems not suitable to store  time series data of Time-of-Flight mass spectrometer semantically.

Is there a more suitable model in OpenChrom to save tof raw data? If not, which interface I can implement?
What I have to do is  acquiring raw TOF data from spectrometer, plotting it and calculating m/z and showing m/z - intensity plot. 
Any comments or suggestion are welcome.


Best regards,

Trig

2016-06-30 0:33 GMT+08:00 Trig Chen <trigchen@xxxxxxxxx>:
Hi Philip,

Thank you very much for the consideration. 
From the wiki https://en.wikipedia.org/wiki/Time-of-flight_mass_spectrometry, the typical value of time-of-flight is about dozens of microseconds. 

Best regards,

Trig

2016-06-29 23:04 GMT+08:00 Philip Wenig <philip.wenig@xxxxxxxxxxxxx>:
Hi Trig,

I thinking switching to nanoseconds will be no problem.
But give me some days to think about possible negative side effects this change could cause. I will give you a feedback until next Monday.


Best,
Philip


Am 28.06.2016 um 15:03 schrieb Philip Wenig:
Hi Trig,

the easiest way would be if we change milliseconds to nanoseconds internally. Honestly, I have designed the scan model to be able to cover a wide range of possibilities. I even thought that milliseconds for retention time is a bit exaggerated. I never thought that it could go far beyond that :-).

The max possible retention time range for chromatograms stored in nanoseconds would be:

2^32 / 2 / 60000000 ~ 35.7 hours

That should be sufficient in any case. I don't think that one likes to evaluate a chromatogram of such a long recording ... despite of the fact that it will be hard to import Terabytes of data.

Let me think about a way how to refactor the code.

Any other thoughts?


Best,
Philip



Am 28.06.2016 um 14:14 schrieb Trig Chen:
We are building our own TOF mass spectrometer and acquiring raw data using a ADC acquisition card with 1GHz acquisition frequency. When acquiring 20us, we got 20000 points of data. The value of point is signal intensity and one point in 1 nanosecond. The ScanMSD model in OpenChrom store m/z and intensity, and ScanCSD model store time and intensity. 

The problem is ScanCSD only accepts integer value millisecond. 
So, which model can I store time of nanosecond and intensity?


Best regards,

Trig



_______________________________________________
chemclipse-dev mailing list
chemclipse-dev@xxxxxxxxxxx
To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/chemclipse-dev


-- 
~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx » http://www.openchrom.net
~~~~~~~~~~~~~~~~~~~~~~~~


_______________________________________________
chemclipse-dev mailing list
chemclipse-dev@xxxxxxxxxxx
To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/chemclipse-dev


-- 
~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx » http://www.openchrom.net
~~~~~~~~~~~~~~~~~~~~~~~~

_______________________________________________
chemclipse-dev mailing list
chemclipse-dev@xxxxxxxxxxx
To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/chemclipse-dev





_______________________________________________
chemclipse-dev mailing list
chemclipse-dev@xxxxxxxxxxx
To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/chemclipse-dev


-- 
~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx » http://www.openchrom.net
~~~~~~~~~~~~~~~~~~~~~~~~

_______________________________________________
chemclipse-dev mailing list
chemclipse-dev@xxxxxxxxxxx
To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/chemclipse-dev


Back to the top