PARADISe user forumExample Category: PARADISeUsing PARADISeusing PARADISe with fast GC-TOF-M …Post Reply

Post Reply: using PARADISe with fast GC-TOF-MS

<blockquote><div class="quotetitle">Quote from <a class="profile-link highlight-admin" href="https://ucphchemometrics.com/forum/profile/jlhdk/">Jesper L Hinrich</a> on April 28, 2023, 9:05 am</div>Hi Andrea,

The answer is pretty simple, PARADISe is build and tested on unit mass data, so<strong> importing from CDF will always round to nearest unit mass. </strong>

We have done some experimentation with non-unit mass, but some issues arise that are not present in the unit mass case. Two of the main issues are,
<ol>
 	<li>The data becomes extremely sparse (many zero values) and the computations have to exploit this to be feasible. PARADISe already does this to some degree, but working with sparse data arrays saved to disk is harder than it sounds.</li>
 	<li>A non obvious issue with high mass spectrometers is at some decimal point, they are no longer trust worth. For example, a fragment might be recorded as both 89.02333 and 89.02332 which then introduces a shift in the m/z axis. Handling such a shift elegantly and robustly is challenging. This issue becomes more present the more decimals you include.</li>
</ol>
Now, you can actually experiment a bit with non-unit masses, but this requires manually setting up your chromatography data as a .mat file. In this file, you need to ensure the m/z axis (variable mz) is given as non-unit mass and the data (variable Data) is of the correct size (it will be big). Then you can import this chromatography data into PARADISe, but the memory requirements and computation will increase significantly. We done some testing with a mass resolution of 0.1 and 0.01 which is manageable for experimentation, but it does require additional patience.

Best,
Jesper</blockquote><br>

Cancel