Tutorial Outline Notebook

[jalew188]

This discussion shares what notebooks we already have using AlphaBase and AlphaRaw.

[jalew188]

1. Basic settings. https://github.com/MannLabs/alphabase/blob/main/nbs_tests/constants already contains notebooks describing the basic settings in alphabase, including atoms (atom.ipynb), isotopes (isotope.ipynb), amino acid (aa.ipynb) and modifications (modifications.ipynb)

2. Mass calculation. Peptide, isotopes, fragments.

3. Introduction of dataframe structure for peptides and their fragments.

[GeorgWa]

I have the following notebooks:
Alpharaw:
Get cycle time, injection times, CV, from a list of raw files for method development

AlphaBase:
Load MSfragger, Maxquant or DIANN PSMs and predict a library

Combine two libraries and repredict all properties with peptdeep.

[jalew188]

Thank you Georg!