I would suggest we provide at least one, ideally two (maybe one small, one larger) sets of files for each of the three main compareMS2 modes (N-vs-N, 1-vs-N and 1-vs-1). For the N-vs-N, they should be phylogenetically interesting, such as the primate or bacterial datasets (currently used for the screenshots). For 1-vs-N, it could be some fish from the food authentication work. And for the 1-vs-1, it could be some pairs of datasets from two different instruments (one low-resolution, one high-resolution). Could be E. coli data, since we have this from nearly all instruments in our labs.
The smaller datasets we can share in Zenodo or OSF already converted to MGF, while we link to raw data in PRIDE for larger datasets.
I would suggest we provide at least one, ideally two (maybe one small, one larger) sets of files for each of the three main compareMS2 modes (N-vs-N, 1-vs-N and 1-vs-1). For the N-vs-N, they should be phylogenetically interesting, such as the primate or bacterial datasets (currently used for the screenshots). For 1-vs-N, it could be some fish from the food authentication work. And for the 1-vs-1, it could be some pairs of datasets from two different instruments (one low-resolution, one high-resolution). Could be E. coli data, since we have this from nearly all instruments in our labs.
The smaller datasets we can share in Zenodo or OSF already converted to MGF, while we link to raw data in PRIDE for larger datasets.