The Stornoway-registered Louisa sank on 9 April as it lay at anchor in calm seas off Mingulay.
The bodies of two crew members were found. The skipper is still missing and presumed dead. A fourth man survived after swimming ashore.
The wreckage of the boat was brought to Clydebank by barge on Tuesday evening.
The Marine Accident Investigation Branch (MAIB) said it wanted to establish why water flooded into the boat and whether automatic alarms that should sound when a leak is detected were activated.
Investigators also want to discover why the Louisa's liferaft failed to release and then did not inflate.
The bodies of Chris Morrison, 27, from Harris, and Martin Johnstone, 29, from Halkirk, Caithness, were found following the sinking.
Skipper Paul Alliston, 42, from Lewis, remains missing despite a massive search.
Only Lachlann Armstrong, 27, from Stornoway, Lewis, survived after swimming ashore.
Investigators are due to begin examining the wreckage of a crab boat which sank off the Western Isles last month with the loss of three fishermen.