TraceFinder 4.0 introduced the ability to perform target analysis on peptide sequences. Given that these chemical analysis methods can be very long (i.e. 3hours for a single sample) and have drastically shifting retention times between samples, TF 4.0 introduced the Extraction Time Window as a peak detection setting.
This new setting allows the user to set a window around where the peak might elute. The default setting is 3 minutes, which means +/- 1.5 minutes from the expected retention time.
This setting may be a bit wide for stable chromatography. A typical setting for the Extraction Time Window is 1 minute or +/- 30 seconds from the expected retention time. This setting can be changed in the Master Method Template or the Local Method. This new setting can then be pushed to all the compounds with two mouse clicks or can be optimized for each target peak, clicking the Three Lined Button in the right coner of the settings page and selecting “Apply current extraction window settings to all peaks in the method”
Since the amount of data being extracted for the targeted peak is reduced, the amount of time per peak analysis is reduced. This setting is separate from the Peak Detection and View Width Window under the Retention Times Tab.
The first tip for speed optimization can be used on any application. On many systems, the power setting is set for Balanced, especially for laptop users as this conserves battery power. However, graphic intense applictions and those applications that require your processor to be run optimally, need the CPU to be fully powered. Otherwise, the CPU and RAM will not perform at their specified speeds.
Under the Control Panel for Windows 7, select the High Performance Option.
Second, Microsoft has put out a new version of the .NET Framework, which drives many of the underlying functions in Windows and applications written for Windows 7. Most people have no idea that this exist.
The new version .NET 4.6.2 fixes many issues Windows was experiencing with .NET 4.5.1, which TraceFinder 3.3 and above was installed with. Also, if your IT group or new PC has .NET 4.6 or 4.6.1, Microsoft has suggested that users install the new .NET 4.6.2.
Below is a link to download the framework from Microsoft. Please check with your IT group before making changes on a corporate PC.
You can check your version of .NET Framework in the Control Panel/Add Remove Programs/Programs and Features