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Re: [chemclipse-dev] Which data model can store the raw data from TOF mass spectrometer?
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



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


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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
~~~~~~~~~~~~~~~~~~~~~~~~

Attachment: OpenChrom-HighRes.png
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