feat: better documentation + example with proteomics integration

[BenjaSanchez]

Areas where we should improve documentation, as raised by @edkerk in a previous issue:

• [ ] Clarify what the input and output parameters refer to for each function.
• [x] Clarify the difference between ecModel and ecModel_batch.
• [x] Provide example of an ecModel constrained with proteomics data.

@IVANDOMENZAIN feel free to edit and add more.