Proteomics Focused Bioinformatics Workshop 2021 - MaxQuant output and Limma results

#ideaproteomics

[svar-xh]

As part of downstream analysis e.g. reactome, I need to use the protein IDs or gene names from my raw data. These downstream analysis dont work when there are multiple IDs per row hence they need to be separated with each protein having its own value. Since there are multiple IDs per row, do you assume that the Reporter intensity corrected value for each protein or gene in a given row is the same?

[noorfatima-gjcb]

Hi, from where we take the data which we use as a input?