I have just released a patch to the Skyline 4.1 release to fix the following issues:

• Fix upgrading 3.7 small molecule document with mixed polarities (thanks to Brian)
• Fix upgrading 3.7 small molecule document to recognize user-provided formula like "C10H30Si5O5H-CH4" as equivalent to "C9H27O5Si5" (thanks to Brian)
• Fix unexpected error handling heavy labeled small molecules (thanks to Brian)
• Increase maximum custom molecule mass from 100 KDa to 160 KDa (requested by Lisa, thanks to Brian)
• Fixed selection in area replicate comparison when grouping by annotation (reported by Shimin, thanks to Tobi)
• Fix missing OK and Cancel buttons in Japanese version of Transition Settings (reported by Tokumaru, thanks to Brendan)
• Fix issue matching newly built spectral library with 4-digit modification precision (thanks to Nick)
• Fix yeast protein details lookup to use new Uniprot interface (thanks to Brian)
• Fix unexpected error with more than 4 isotope label types (thanks to Nick)
• Fix unexpected error for invalid prefix or suffix during import results (thanks to Kaipo)
• Fix unexpected error in Peak Area CV toolbar (thanks to Tobi)
• Fix unexpected error DDA retention time alignment (thanks to Nick)
• Fix unexpected error "item with the same key already added" editing custom molecule (thanks to Nick)
• Fix two modifications defined on the same amino acid can cause an error "The expression 'C''2H6N'' is not a valid chemical formula" (reported by Rich, thanks to Nick)
• Fix handling when there are zero spectra in the spectral library to load and not cause an error (thanks to Nick)

Otherwise, now is a great time to upgrade to 4.1. Though it requires installing over your current Skyline, which you can do from the website installation page.

--Brendan