Problem Dataset

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Nicholas David Clark

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Aug 29, 2023, 3:26:00 PM8/29/23
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I have a SEC-SAXS dataset which is quite troublesome, due to the odd background intensities (see attached images). I've tried to process the data with REGALS but am unable to correctly deconvolute the signals. 

I'm wondering if anyone has dealt with similar data in the past and has some insights into how to properly proceed with processing? Alternatively, is the data just useless in this state and I'm better off recollecting?

Thanks,

Nick
mean_intensity.png
integrated_intensity.png

Jesse Hopkins

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Aug 29, 2023, 5:38:56 PM8/29/23
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Hi Nick,

Any time you're asking the question of whether you should recollect data, I tend to say that you should go ahead and do that if possible (especially if you can figure out what was causing the baseline drift and how to get rid of that). That being said, there's a couple of options here, especially for the stronger signal data.

First, you might be able to use a buffer region just before the first small peak, and then do a linear baseline correction across the peaks, just on the downsloping side. If you make the range tight enough, there might not be that much drift, allowing you to get something that might be more reliable.

Second, REGALS can take a lot of playing around with. I'd recommend trying it both with and without subtracting buffer (e.g. fitting the buffer as a component, as well as the drift), and limiting the range for REGALS to where it starts to increase, around frame 215. You might also try cutting off some of the early frames and seeing what affect that has (basically trying to limit the amount of change that you're fitting).

If you send me the dataset I can take a quick look at it when I have time.

All the best.

- Jesse

----
Jesse Hopkins, PhD
Deputy Director
BioCAT, Sector 18
Advanced Photon Source


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Nicholas David Clark

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Aug 30, 2023, 7:43:47 AM8/30/23
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Hi Jesse,

Thanks for the recommendations and the offer of assistance! I've sent you the dataset off-list.

Best,

Nick

Jesse Hopkins

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Aug 31, 2023, 10:07:52 AM8/31/23
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Just to close the loop on this question, we determined that the data hadn’t been properly normalized. After applying the correct normalization, the integrated intensity looks like you’d expect for a SEC-SAXS dataset.

All the best.

- Jesse

----
Jesse Hopkins, PhD
Deputy Director
BioCAT, Sector 18
Advanced Photon Source

Nicholas David Clark

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Aug 31, 2023, 10:16:29 AM8/31/23
to BioXTAS RAW
Should anyone run into a similar issue (Panel A), Jesse figured out that the main issue was incorrect scaling of the water peak (normalization) during the series. We determined this by decomposing the series into the component profiles, at which time it became obvious that the scaling was poor (Panel B). We scaled to the water peak in RAW (Panel D) and then exported the correctly scaled profiles. We then replotted the series in RAW from the exports and the series now should be usable (Panel C).
ScalingFix.png
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