Decreasing Run Time when Using the LCMS Reconstruct Algorithm in ProteinPilot™ Software

For research use only. Not for use in diagnostic procedures.

Answer

In order to decrease the time needed when using the LSMS Reconstruct algorithm in ProteinPilot™ software, a configuration file must be modified. Users will need to locate the ProteinPilot.exe.config file located in the following directory: C:\Program Files\AB SCIEX\ProteinPilot.
This configuration file should be opened with Notepad++ software and then the following line should be added: 
<add key="MemoryUsageGigabytesPerSlice" value="1"></add>
A value of 1 or 2 should be appropriate. 

The use of a large amount of computer memory when running this algorithm is due to large time stripes in the LCMS reconstruct. A fix was added to the ProteinPilot software application in the SCIEX Cloud Platform that caps the maximum size of the time stripe to 10 min. However, ProteinPilot software installed on a desktop PC still tries to automatically calculate the ideal time stripe. With data from a TripleTOF® 6600 LC-MS/MS system, the calculated time stripe can be very large (>10 min). This leads to calculations that are very computationally intensive and long. The adjustment to the ProteinPilot software configuration file indicated above indirectly forces narrower time stripes and improves the overall processing time.