We have had problems with the new version as well using command line sequest.
Searches run OK, but the sequest_summary gives anomolous results.
A possible explanation may be that the header format has been altered.
(see below):
New version
>From Owl v30.2:
>owl||LAC_HUMAN IG LAMBDA CHAIN C REGIONS. - HOMO SAPIENS (HUMAN).
QPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQ
SNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
>average mass (m+h)+ = 11237.5
Old version
>From Owl v30.1:
>LAC_HUMAN pir|P01842| IG LAMBDA CHAIN C REGIONS. - HOMO SAPIENS (HUMAN).
QPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQ
SNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
>average mass (m+h)+ = 11237.5
-Elliott Nickbarg
!