Understanding the MSstatsPTM input

[Joaquin Reyna]

Hi MSstatsPTM team,

Thanks for building MSstatsPTM. I was recently asked to use this as part of a collaboration with my proteomics core, so please forgive me if I miss any details.

As I've been going through this package I have found it difficult to understand the underlying input data structure. At a high level, I understand this software/statistical framework is trying to correct for protein-level changes by integrating data from two experiments:

1) Global protein data
2) Phosphopeptide data

As such, I was imagining the input to MSstatsPTM would be either two separate files, one for each experiment, or a single file that concatenates these two datasets together. Is this correct?

I don't see any vignette mention this, which makes it difficult to understand how to get started. I'm wondering if you could provide more documentation on the expected input format, either through additional vignettes or a detailed GitHub README.

Many thanks,
Joaquin