Dear Skyline Team,

I am a quite novice in mass-spec field,
but I plan to do label-free (relative) quantification of entire proteomes between different strains of bacteria (S. aureus).
If I correctly understand, MS1 Filtering using DDA data should work for our purpose.
But I have also noticed a paper that describes DIA-based quantitative proteomics for the species of our interest (They do not use Skyline, though).
https://www.ncbi.nlm.nih.gov/pubmed/28887440
Because a spectral library for DIA analyses are provided in the work,
I am wondering if just running DIA experiments might be a better choice than DDA/MS1-filtering method.

Which is a recommended strategy in terms of
> quantification abilities such as accuracy, precision, and reproducibility (Note that we are going to use Q-Exactive Plus).
> ease of data analyses with current version of Skyline software.

I greatly appreciate any suggestions/comments on the issue.

Best regards,

nakaokah2