Clean Mass Spectrometry Data in 4 Steps

In this video, I will demonstrate how to convert basic data cleaning methods into functions that can automate the cleaning of mass spectrometry data. I will also showcase the effects of cleaning by performing Principal Component Analysis (PCA) and plotting score plots. This will allow us to evaluate the effectiveness of the cleaning process in clustering gram-negative and gram-positive bacteria. This is the fourth video in the mass spectrometry data processing series, and in the previous videos, we have covered peak peaking, signal filtering, and baseline correction techniques using Python and Scipy.
Github: github.com/chr...
peak_picking: • 2 Methods to Find Peak...
baseline correction: • How to Baseline Correc...
Signal Filtering: • Analytical Signal Proc...

[@toylemmons9320]

Yes, my brotha! Keep it up!

[@CJP3]

Thanks Bro! ✊🏽

[@CJP3]

Hey, have you subscribed? 😅

[@tejeshwvardhan1165]

finally a useful thing . great!

[@CJP3]

Hi! Thanks for the kind words! I’ll be focusing a lot more on real scientific research data.

[@Haav89]

Does this mean that all the data samples have exactly 54 peaks? or is this the maximum number of peaks on a signal and the rest are Null padded?

[@CJP3]

Howdy Hugo, In this case, all the samples will have 54 peaks. Any peaks found in one sample will be located in the other samples even if it did not initially meet the criteria. Many commercial software applications take a similar approach.

[@muhammadharsanto2024]

Hello, professor, may I see your data? It'll really help my understading I think. Thank you very much.

[@muhammadharsanto2024]

or maybe the types of headers and the first column

[@CJP3]

@@muhammadharsanto2024 I was reviewing this video and didn't realize until I read your comment that I didn't show the data table until relatively late into the video (sorry). A view of the data table can be seen at 5:44 then as it is transformed I continue rendering the updated table to the screen.

[@muhammadharsanto2024]

Thank you Professor
@@CJP3