Modifications aren't specified on the command line, they're taken from what;s found in the input file.
Of the command line options found here:
Skyline uses "-H", and "-o" and may use "-c", "-l", "-a", "-i", and "-E" depending on your settings.
Thanks for using the Skyline support board,
-o Overwrite existing library. Default append.
-S <filename> Read from file as though it were stdin.
-s Result file names from stdin. e.g. ls *sqt | BlibBuild -s new.blib.
-u Ignore peptides except those with the unmodified sequences from stdin.
-U Ignore peptides except those with the modified sequences from stdin.
-H Use more than one decimal place when describing mass modifications.
-C <file size> Minimum file size required to use caching for .dat files. Specifiy units as B,K,G or M. Default 800M.
-c <cutoff> Score threshold (0-1) for PSMs to be included in library. Higher threshold is more exclusive.
-v <level> Level of output to stderr (silent, error, status, warn). Default status.
-L Write status and warning messages to log file.
-m <size> SQLite memory cache size in Megs. Default 250M.
-l <level> ZLib compression level (0-?). Default 3.
-i <library_id> LSID library ID. Default uses file name.
-a <authority> LSID authority. Default proteome.gs.washington.edu.
-x <filename> Specify the path of XML modifications file for parsing MaxQuant files.
-p <filename> Specify the path of XML parameters file for parsing MaxQuant files.
-P <float> Specify pusher interval for Waters final_fragment.csv files.
-d [<filename>] Document the .blib format by writing SQLite commands to a file, or stdout if no filename is given.
-E Prefer reading peaks from embedded spectra (currently only affects MaxQuant msms.txt)