It appears that the problem is that BiblioSpec does not support Chlorine in MaxQuant results.
If I run BlibBuild.exe with the additional "-v warn" command-line argument, I get a helpful warning message:
> BlibBuild.exe -v warn msms.txt mylibrary.blib
Reading results from msms.txt.
WARNING: Unknown element for 'C(21) H(17) Cl F(2) N(4) O(2)': 'Cl'
ERROR: No matching mod for ARS in sequence VVGAC(ARS)GVGK (line 8). Make sure you have provided the correct modifications[.local].xml file.
For some reason, the only elements that BiblioSpec supports for MaxQuant are H, O, C, N, P, S, and Na.
BiblioSpec also supports the heavy elements "Hx", "Ox", "Cx", and "Nx", along with the synonyms "2H" and "13C".
I will ask around and see whether we can fix this.
-- Nick