Module 4 F.A.Q.

4.1 General

How do I cite ProteoMill?

Martin Rydén, Martin Englund, Neserin Ali, ProteoMill: Efficient network-based functional analysis portal for proteomics data, Bioinformatics, 2021;, btab373, https://doi.org/10.1093/bioinformatics/btab373

Is ProteoMill free?

Yes.

Is ProteoMill’s source code publicly available?

Yes, the code is available here: https://github.com/martinry/ProteoMill

ProteoMill displayed an error message or the application stopped working. How do I report it?

Please submit a new issue at https://github.com/martinry/ProteoMill/issues, label it as a bug and describe the event.

I have an idea for a new feature that I think would be useful in ProteoMill. Where can I post it?

Please submit your idea to https://github.com/martinry/ProteoMill/issues and label it as an enhancement.

How was ProteoMill developed?

ProteoMill was developed using R, shiny and a long list of other R-packages. ProteoMill is hosted as a web-app using Amazon web services.

4.2 Network analysis

I have selected a protein in the volcano plot, but it doesn’t show me its interactors in the network plot.

The protein may be excluded from the network plot because it doesn’t fulfill the requirements set under “Network settings” or “Selection criteria”.

  1. Set “Subset by up- or down-regulation” to “Both”.
  2. Set “Minimum abs. log2FC” to 0.
  3. Set “Interaction confidence” to 0.