Category Archives: Troubleshooting
Issues with Actively Scanning Virus Protection Applications and Data Acquisition and Processing
In many instances of instrument and processing stations being connected to the internet, I’ve helped individuals having system lock up issues on various mass spec systems over the past 20 years, when using Real-Time Virus Scanning Protection.
This issue is vendor agnostic and will causes problems in data collection and processing on a number of vendor platforms.
If you have Norton, McAfee, Microsoft Security Essentials/Windows Defender, etc and you need to run real-time virus protection. You should exclude the folders where data is actively being collected and processed. This will ensure that any processes, such as instrument communication, raw data writing to disk or processed result file creation,aren’t being interrupted by virus checking during data collection and manipulation.
Below is a list of folders recommended for exclusion in the various anti-virus programs.
The example comes from Windows Defender in Windows 10, and will have a different user interface dependent on what application you are using, however each application available commercially today has this capability.
1:Real-time protection is on and select settings
2: Select Add an Exclusion
3: Add each of these folders as an exclusion
Tip for Optimizing the Speed of Processing Data for TraceFinder 4.0 and later
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.
Peak Extraction Window
Tips on Optimizing Speed for TraceFinder4.0 and later
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.
High Performance Power 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.
.NET Framework Offline Installer
You can check your version of .NET Framework in the Control Panel/Add Remove Programs/Programs and Features
Add/Remove Programs .NET Version
TraceFinder 3.2 – Method Setup Tweak – Threshold Setting
There have been a few questions on the issue of peaks not being integrated, while performing quantitation, although the signal is strong. A reason could be that when a compound is created in the method, it has a related compound database entry for a threshold setting. This setting is used in targeted screening but is not editable in quantitation mode.
The setting has a default value of 5000 for calculated peak area. This setting does have a global override in the Local and Master method Processing section. The default value is unchecked and blank. This means the default threshold is 5000 for all peaks. If you are having an issue where the peak is not integrated but has a strong signal, then change the setting by checking the box and entering a new value such as 0 or 500. The data will need to be reprocessed as this value is not automatically applied.
TraceFinder 3.2 – New Instrument Method Managed Location
In previous versions of TraceFinder, the Instrument Method utilized for data collection was required to belong in the c:/Xcalibur/Methods directory folder.
In TraceFinder 3.2, the new location for the Instrument Methods is located under the C:/TraceFinderData/Instrument Methods directory folder.
Since TF has is a “managed systems”, meaning that we provide the unique capability of synced updates and other functions the Instrument Method, we have a need to know where the method is at all times.
Therefore, the use of the managed directory is a requirement. By moving the Instrument Method for TraceFinder into it’s unique folder, it allows you the freedom to use any folder for method development purposes.
When you have the final version for use in data collection simply save the “.meth” file into the C:\TraceFinderData\Instrument Methods directory folder, so that it will be used as a template for all the sample sets going forward.
Troubleshooting – Windows 7 Themes Performance Issues
Change the theme to improve performance
If your computer is working slowly, you might see a message saying that the theme is using most of its allowed memory. If this happens, you can change to the Windows 7 Basic theme or a high-contrast theme to improve performance.
If you change the theme to Windows 7 Basic, you will no longer get the full Aero experience. Aero is the premium visual experience in this version of Windows. It features a transparent glass design, window animations, Aero Flip 3D, and live window previews.
To change the theme
- Open Personalization by clicking the Start button
, and then clicking Control Panel. In the search box, type personalization, and then click Personalization. - Under Basic and High Contrast Themes, click Windows 7 Basic or one of the High Contrast themes.
Issue with Column Arrangement in Data Review-How to Avoid and How to Fix
Some have experineced an issue when starting the application after rearranging columns in data review.
They recieve a .Net framework error that states that columns have been arranged to the left of frozen columns.
This is a known issue that will be fixed in the next version of TraceFinder.
To avoid the issue the columns in the image below should remain the farthest to the left on the data review grids.
If you experience the issue, rename the file tracefindersettings.sqlite to TraceFindersettings_old.sqlite and restart the application.
The factory default settings backup file will be automatically recreate the tracefindersettings.sqlite file.
The image below shows the directory path to the file.
Note that the directory path is dependant on the version of TraceFinder that it is installed.
My Filter String Is Missing After I Updated My Methods Associated Rawfile.. HMMMMMM
So in both the local and master methods, a user can update the associated rawfile to see the peaks they are looking for.
This dialog has an option to update the filter strings. Which makes it easy to do especially if you have hundereds of compounds.
When you do this, the logic looks to the compound database info that is in the Acquisition list and to help it determine the filter with the right precusor and then the extracted ion setting to see which filter contains its value within the range of product ions in the brakets of the mass filter. If everything matches from the newly selected rawfile it sets the filter accordingly. If it doesn’t then the compound will have a little red dot next to its name and a missing filter error lights up.
This typically occurs when the new file has a slightly different filter string and the method’s extracted mass falls outside of the product mass range of the filter.
The following video shows you how to manually fix this issue.
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
Need to Share Data – Here’s a Freebie from Microsoft
So we’ve had a couple of people want to send data across to help them look at methods and such, but they were limited by the amount of storage on dropbox or the security concerns of an outside source.
Here is a link to signup for Microsoft’s SkyDrive
This gets you 7 Gigs of storage right off the bat. No money required. The beauty of this is that it can sync with all your MS Office applications, which you can share or keep to yourself.
It also works as a location on your desktop so you don’t have to ftp large files, simply drag and drop.
The really cool part about this is, if I have a iPad or other mobile device and use the SkyDrive app, I can edit my stored documents real time in the cloud. I have access to them from anywhere at anytime, and anyone I have shared the document with can collaborate in real time.
For all those of you with large data sets this is a great spot to shared the files, and it works with your intergrated Windows security just as if it was a mapped drive.
Excel rules the world or at least it thinks it does…..
So, this week we’ve gotten a few questions on importing a sample list in CSV format.
There is an error that can occur if the csv file you exported and made adjustments to, is still open in Excel when you try to reimport it.
Unfortunately, the error message isn’t as descriptive as maybe it should have been, but it did give us a chance to post another answer to a “Ask A Guru” question
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
TraceFinder: Direct Knowledge 