Identification of m/z differences in 2 different ROI

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Marco Fidaleo

Jun 6, 2024, 12:10:20 PMJun 6
to Cardinal MSI Help
I aim to adopt a different approach akin to gene expression analysis. I would like to identify and select two ROI within one biological sample. Subsequently, each pixel encompassed by the selected ROIs will be treated as an individual sample and each peak in the spectrum as a gene.  This will enable me to generate volcano plots, facilitating the visualization of differences in specific m/z values across the samples.

I wonder if Cardinal supports such analyses. However, if not, I would like to generate a matrix where each row has info regarding the ROI, the pixel, the peaks and their intensity. This matrix will then serve as the basis for subsequent analyses. Is this possible?

Jason Rodencal

Jun 6, 2024, 12:21:17 PMJun 6
to Cardinal MSI Help

You can select ROIs in cardinal datasets in Cardinal v3.6. Then, it is fairly simple to assign labels or factors to the relevant pixels. If Cardinal doesn't support the analyses you want, then I imagine it should be relatively easy to export the matrix with the labels, although I couldn't tell you how to do this personally (still a novice here). The main weakness of the ROI selection is that it relies on manually drawing regions, and can be difficult to zoom during the process, so small regions could be hard to capture manually. If you figure out a solution for that please feel free to share.

The process is discussed in detail in this youtube video, beginning at 1 hr 41 min:


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