Hey all! I have a question about my proteomics data evaluated in Proteome Discoverer. I got three volcano plots of three biological groups in a ratio with control group. In one group I see a strange pattern, while other two look normally. Log2 ratio is somehow 100% -related to p-values with no exception (please see the graphs). Obviously it is not the issue of plotting itself, but in calculating the ratio or the p-value. Quantification was done using non-nested design, label-free quatification, pairwise-based ratio calculation, t-test, normalization of total peptide amount.
Does anyone knows the reason for that pattern?
Thanks a lot!
I suggest you take a look at the paper below. It has some funky looking plots and why they look funky. They do not have your exact "problem" but references therein may point you in the right direction.
Also, Google is your friend. A quick search and I found a Volcano plot the same as yours. It does not mean it's right, but it's something that you can search for and see if it's common and maybe when it occurs.
M.-H. Lin, P.-S. Wu, T.-H. Wong, I.-Y. Lin, J. Lin, J. Cox, S.-H. Yu, Benchmarking differential expression, imputation and quantification methods for proteomics data, Briefings in Bioinformatics. 23 (2022) bbac138. https://doi.org/10.1093/bib/bbac138.
https://biocorecrg.github.io/CRG_RIntroduction/volcano-plots.html
Hi Jan Gebauer ,
Same thing happened to me recently. I thought it was kind of a glitch and I was the only one. Have you found a reasonable explanation so far? I would be very grateful if you could share it.
Thank you for sharing Peter G Hains
Hi Jan Gebauer
I've also had some funny looking volcano plots from PD data. Discussion here: https://www.researchgate.net/post/Artefact_in_volcano_plot
I never got to the root cause, but the funny lines of points lining up were an artefact of normalisation - mind you, the underlying table of PSMs from PD was the original source.
Unfortunately I never got around to identifying why PD gave odd output.
Sorry I can't be more helpful!
Sam
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