The UniProt complete proteome file is in fasta format and indeed does not contain information on how the isoforms differ from the canonical sequences.

However, the flat file format of the canonical isoform entry does contain the information: e.g. http://www.uniprot.org/uniprot/P28223#section_alternative (html view) or http://www.uniprot.org/uniprot/P28223.txt (flat file):

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=P28223-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=P28223-2; Sequence=VSP_044593, VSP_044594;
CC         Note=No experimental confirmation available;
..
FT   VAR_SEQ       1     54       MDILCEENTSLSSTTNSLMQLNDDTRLYSNDFNSGEANTSD
FT                                AFNWTVDSENRTN -> MQFLKSAKQKPNYYHIMLVEDQEE
FT                                GTLHQFNYCERCSESQNNKCISCVNPEDKW (in
FT                                isoform 2).
FT                                /FTId=VSP_044593.
FT   VAR_SEQ      55    138       Missing (in isoform 2).
FT                                /FTId=VSP_044594.

See this page for documentation: http://www.uniprot.org/manual/alternative_products

Check Ensembl Transcripts for this purpose.