There are some limits when you do "Import Fasta", but the intention of those limits is to protect you in case your digestion or filter settings are going to result in an unexpectedly large Skyline document.
If you've told Skyline to only include peptides that are in your spectral library, then these limits do not apply. That is, if it says either "Library" or "Library and Filter" at "Settings > Peptide Settings > Library > Pick peptides matching" then Skyline does not limit the number of peptides or transitions that you get when you do "File > Import > FASTA".
The limits are 5 million transitions and 200,000 peptides.
The other time that this limit applies is if you have "Auto-select all matching peptides" selected at "Settings > Peptide Settings > Filter" and you do somethign which changes the set of peptides in your document.
These limits used to apply in more cases, but since that time we have added a Cancel button to most operations which might take a really long time and result in a Skyline document that is too large.
thank you very much for the explanation.
In general i would find it always nice to have warning messages instead of fixed limits, especially with the new computational tools coming up which deal with a much higher number of PTMs.
Also, Skyline is extremely helpful to build the Input for Prosit. Its nice if the limit is lifted once a library is available, but in this context the limit might prevent building a large library in the first place.