DSP Protein Analyses [discussion]

[nickhsmith]

Hello, my name is Nick, and I am new to working with DSP proteomics. I am interested in running differential expression analyses for proteomics data, and I was so happy to come across this package (I have the bioconductor version standR_1.10.0) . I know that the vignette/walkthrough was for RNA-seq data, and there are some notable differences with the assumptions that don't hold for proteomics data. In your 2023 paper you highlight the importance of generating and improving DSP proteomics workflows.

I was wondering if you have any recommendations or suggestions for proteomics data, namely normalization and differential expression strategies compared to RNA-seq inputs.

Thanks in advance!

[ningbioinfo]

Hi @nickhsmith . For protein DSP data, I would use the sizefactor as the normalization method, and kept the differential expression pipeline as it is for now, check out https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1135489/full.