OMICtools is a neat directory of tools and resources for OMICS type analysis. I found this one on the web when writing a review manuscript. It did a ton of good for my manuscript and I found that most of the tools our bioinformaticians were developing were already out there.
I found a section on Proteomic software tools and databases.
Mass spec-based proteomics is a separate section.
I was more interested in the proteogenomics tools section.
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