UPDATED: Extraction of LC/UV data

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Hi,

I spent the past few hours in search for a free software that will allow me to extract UV data from a Thermo Fisher Scientific Xcalibur *.RAW-file. I came across numerous tools for inspecting the MS-data from that file, but I have no idea how to access its UV-data. I would be fine if I could just export the data points from the UV-scans to a text file or something.

Any help is appreciated! :D
Why I was asking:

I ran a gradient from a less polar solvent (A) to a more polar one (B) on a reverse phase column. I observe a severe baseline-drift (not a linear drift, but like this like this). If I am not mistaken, the drift has to come from the UV-absorbtion of B.

MS data shows that during this drift, a substance is eluted (that substance dissolves well in B). The drift seems to swallow the peak of the substance. Also, I doubt that this would be a nice peak, since the elution of the substance stretches over several minutes all along the gradient.

UV data was collected using a diode array detector. Now I was thinking that it should be possible to retroactively choose a different wavelength to calculate the peaks from, so I might at least be able to iron out the drift. Does this work?

Is there a way to find out which wavelength was used for detection?
As far as I know, Xcalibur is MS software, so it would not have any PDA capability.
If it's a current Thermo instrument, the UV detector would be run by Chromeleon. Older ones by Thermoquest (?).
-- Tom Jupille
LC Resources / Separation Science Associates
tjupille@lcresources.com
+ 1 (925) 297-5374
Hey Tom,

thanks for your answer. In Xcalibur you can inspect the MS and UV scan at any time of the run, so I just assumed that that .raw file would also hold UV data.

How are peaks calculated when using a PDA detector? Do they still come from one certain wavelength or from the whole spectrum?
I don't have any experience with Xcalibur, and the fact that you can use it to look at the UV spectra makes me suspect I may have given an incorrect answer. Probably best to check with Thermo tech support.

To answer your second question, I do know that Empower has a "maxplot" functio, which plots the maximum absorbance it sees at any wavelength as a function of time. Roughly analogous to TIC in LC-MS. I (obviously) don't know whether Xcalibur has something similar.
-- Tom Jupille
LC Resources / Separation Science Associates
tjupille@lcresources.com
+ 1 (925) 297-5374
If you have Xcalibur, why not just use it (and if you haven't, see below)? Yes, the one data file contains both the MS and PDA data. PDA data are treated very similarly to mass spec data: in Xcalibur's "Ranges" menu for chromatograms, if you specify PDA as the detector, it will default to total wavelength chromatogram (just as MS defaults to TIC), but you can also specify a chromatogram over a chosen wavelength range (exactly as you can specify an extracted ion chromatogram over a chosen mass range).

The PDA pretends to be a fixed-wavelength detector too, so if the original method had channels at known wavelengths as well as spectra, the drop-down box for detector in "Ranges" will have UV and PDA listed separately. If you choose UV, the options will be "Channel A", "Channel B" etc.

The thinking behind this was that you can save disk space by collecting spectra fairly rarely for qualitative purposes, but monitor your favourite wavelengths much more frequently, for good quantitation.

In quantitative processing methods, you can specify any detector including PDA and UV as the signal you'd like to use for quantitation, and from this, you can specify any channel (UV) or any wavelength (PDA).

Thermo seem to be being quite generous about Xcalibur, probably realising that offering easy access to data-handling gives them a significant sales advantage over other manufacturers when it comes to selling instruments, which is ultimately where the money is. Do a Google for Xcalibur demo download and you'll find it.
Hi, gamma!

Did you happen to find a solution to your problem? Could you share it?

Thanks!
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