ProteinLynx Global Server (PLGS) is slow processing; nonspecific sequence databank - WKB5677

SYMPTOMS

• PLGS takes a very long time to run searches (see PLGS job manager)
• In Task Manager, iadbs.exe (the MSe search) opens, but it then takes a long time to run the search and shut down

ENVIRONMENT

• ProteinLynx Global Server 2.x.x
• ProteinLynx Global Server 3.0
• ProteinLynx Global Server 3.0.1
• ProteinLynx Global Server 3.0.2
• ProteinLynx Global Server 3.0.3

CAUSE

Multi-species or high redundancy protein sequence databank is used in search workflow.

If the sequence databank being used is not specific to the species from which the samples were derived, or if it contains a lot of redundant sequences, the search step will be slower.

In addition, if you try to use the entire Uniprot database as a library, it may overwhelm the PC's RAM.

FIX or WORKAROUND

1. Download a fasta file from Uniprot that is species-specific and doesn't contain redundant sequences (e.g., fragmentary sequences derived by automated translation of genomic DNA), import it into the PLGS databank library, configure a workflow that uses the new databank, and repeat the search. (See PLGS help files for instructions.)
2. If there are any existing libraries made from the entire Uniprot database (look on the PC for very large fasta files with problems), remove the associated protein sequence databank from the PLGS libraries editor and restart PLGS.

ADDITIONAL INFORMATION

There are many factors that can contribute to PLGS 3 processing MSe data slowly. Several of these issues may occur simultaneously, which can have an additive or synergistic effect that slows processing down even more. If the above solution does not help, try the others, either on their own or in combination with this solution.

See articles 5378, 5380, 5382, 5386, 5388, and 5679.