Data conversion fro xcalibur raw to netcdf

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5 posts Page 1 of 1
Hi Guys,
I am writing to ask for help to resolve the issue that I am facing with the xcalibur raw file conversion. I did used the xcalibur tool to convert the file to netcdf format. However, when I open the net cdf file using appropriate software, instead of showing me the averaged total ion chromatogram (TIC) (having Gaussian peaks), it shows me a TIC where the single composite chromatography peak is made of several small peaks (probably single scans) which is something similar to what we observe when we open a raw xcalibur file on qual browser before applying the scan filter.
Any help will be really appreciated.

Thank you.

Sincerely,

Alpesh
Hi Guys,
I am writing to ask for help to resolve the issue that I am facing with the xcalibur raw file conversion. I did used the xcalibur tool to convert the file to netcdf format. However, when I open the net cdf file using appropriate software, instead of showing me the averaged total ion chromatogram (TIC) (having Gaussian peaks), it shows me a TIC where the single composite chromatography peak is made of several small peaks (probably single scans) which is something similar to what we observe when we open a raw xcalibur file on qual browser before applying the scan filter.
Any help will be really appreciated.

Thank you.

Sincerely,

Alpesh
I haven't used Xcalibur for a while. Are you using the readw file conversion tool? If not, you could try it. Back when I used Xcalibur, it was the tool I used, but every time Xcalibur was updated, I experienced exactly the problem you had. Usually updating to the most recent version of readw solved it. It was annoying! Readw back then also needed the Xcalibur developers kit, which is installed automatically when Xcalibur is installed - but it meant readw didn't work on any other PC. I have no idea how relevant all this is (if at all), but post in case it helps! good luck!
There are two ANDI specifications:
ASTM E-1947 - for pure chromatographic data
ASTM E-1948 - for MS data

Probably your final software improperly understands MS data exported according E1948 specification.

The TIC in this format is an array of samples with exact time for each sample. Of course each TIC sample accompanied by mass-spectra.

IMO your software improperly displays properly exported data. TIC has to be painted as smooth curve. It can be very angular because of small MS-scan rate - so at every TIC peak you get 3-5 scans instead of 10-50 for generic GC.

P.S.
Btw - could you drop a link to couple of Thermo RAW file samples. We are testing in our UniChrom the MS import (made it month ago without any Xcalibur and ReADW and being cross-platform).
The problem probably isn't the rate of collection of spectra, it's more likely to be that Xcalibur piles up all its spectra in one file. The original poster mentioned how the chromatograms appear in QualBrowser before using a scan filter. This suggests that (s)he is using a system that produces MS2 and MS data. As a result the file might contain
MS 200-2000
MS2 on precursor ion 943.1
MS 200-2000
MS2 on precursor ion 451.1
MS 200-2000
MS2 on precursor ion 943.1
... etc.
Since the TIC for the full MS 200-2000 is much greater than the TIC from an MS2 spectrum, if you merely plot the TIC for all scans irrespective of what they actually are, you get a chromatogram that bounces up and down, high for the MS, low for the MS2, but the high-points follow a general peak-shaped envelope. QualBrowser has scan filters that allow it to pick out just the MS spectra, and create a TIC from them, which is then the right shape. Better format-converters and software can understand what's going on, and select the right spectra. Naïve software will assume all spectra are equal, and get confused.
It's also unfortunate that manufacturers don't tend to be very outward-thinking in their raw data formats. The problem for 3rd-party software is that it might work now, but there is always the chance that next week Thermo will release something new that creates files that aren't handled properly by the 3rd-party software, and suddenly as a user you've got a whole lot of trouble - at the very least you have to wait a few months while 3rd-party developer catches up, or at worst you're faced with a choice of trying to back-track on your instrument software (and oh look! when we reinstall the previous version it won't recognise the firmware on all the instrument modules, and the engineer has gone off with the firmware upgrade disks...), or losing the data-handling pathway. If you need 3rd party software, I think it's really important to batter the original manufacturer until they provide a means of conversion that actually works. But even then, life isn't simple. Open formats by definition have to cope with whatever data-set the mass spec produces, so there is still a possibility of misunderstandings between how the manufacturer thinks their data should be packaged into mzXML, and how the 3rd-party software expects it to be packaged.

By the way, I'm stupid: if at all possible, abandon net cdf and use mzXML or mzData, and the problem will go away. I'd bet a chocolate bar on that, and I'm not a betting person generally.

Sorry to write at length. File formats are a touchy subject for me.
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