u/MilkF5

I have been working in proteomics for about 5 years.

Recently, I had a discussion with my supervisor about why proteomics journals usually have relatively low impact factors.

To be honest, I avoided submitting to these journals for years because of that. We usually preferred broader biomedical journals.

But recently I changed my mind a bit. I submitted two papers to Proteomics and one to Journal of Proteome Research.

Now I wonder if impact factor is a bit misleading in this field. Proteomics is very important, but many papers are technical, dataset-based, or useful mainly to a specialized audience.

The same proteomics study may get more attention if it is published as a cancer, immunology, metabolism, or microbiology paper instead of as a proteomics paper.

So I am curious:

Do you think proteomics journals are undervalued?

Do you avoid specialized journals because of impact factor?

For people working in proteomics or other omics fields, how do you choose where to submit?

I have been reading a lot of recent proteomics papers, especially LC-MS/MS quantitative proteomics studies, and I keep getting the impression that most downstream bioinformatics workflows are basically the same.

A typical pipeline seems to be something like:

preprocessing/filtering of protein or peptide abundance matrizes
normalization, often VSN, median normalization, quantile normalization, etc.
missing value imputation, usually MinProb, random forest, KNN, QRILC, or some variant
differential abundance analysis with limma, MSstats, DEP, proDA, DEqMS, or now newer tools like limpa
volcano plots
heatmaps/PCA
clustering, sometimes Mfuzz
co-expression/module analysis, sometimes WGCNA
ORA/GSEA/pathway enrichment
STRING/Cytoscape protein-protein interaction networks

And then the biological interpretation is usually based on enriched pathways, hub proteins, or interaction networks.
My question is: is there anything genuinely new or methodologically interesting happening in proteomics bioinformatics, especially downstream of protein quantification?