median normalization for proteomics
The kind of normalization depends on what you what to explore. So, there is no absolute answer to this. Different normalizations highlight different aspects of your dataset. There is a nice paper for a higher throughput quantitative study that I would recommend reading:
Nusinow, David P., John Szpyt, Mahmoud Ghandi, Christopher M. Rose, E. Robert McDonald 3rd, Marian Kalocsay, Judit Jané-Valbuena, et al. 2020. “Quantitative Proteomics of the Cancer Cell Line Encyclopedia.” Cell 180 (2): 387–402.e16.
What you want to aim for is a normalization that removes batch effects and that clusters together your quality control samples that you know are very similar to each other.