Tips and Troubleshooting Hints

 Parameter Files: What happens if you don't put in a parameter file name in the ZNova Params field of the Xcalibur sequence? ProMass will use the znova.params file in your ZNova install directory (e.g., C:\Program Files\ProMassXcali\ZNova\znova.params). So if you don't like having to add parameter files to your Xcalibur sequence, just edit the default znova.params file and leave the ZNova Params field blank in your Xcalibur sequence.

 Comprehensive Deconvolution Mode: When should you use the comprehensive deconvolution mode? If you are dealing with complex spectra, where the multiply charged series potentially overlap, use comprehensive mode.  As it turns out, comprehensive mode should be used most of the time for "real world" spectra.

 Internet Explorer security warnings when viewing ProMass data:  ProMass employs Javascript in many of the web-based report pages to allow dynamic sorting of tables and various other features.  Unfortunately, Internet Explorer may disable some of these features in attempt to enhance web browser security.  If this happens, a warning message will be displayed "To help protect your security, Internet Explorer has restricted this webpage from running scripts or ActiveX controls that could access your computer. Click here for options..."  You can choose to allow the blocked content, however, the security warning will be displayed each time a new ProMass report is displayed.  The method discussed below shows you how to set Internet Explorer to enable these Javascripts to run properly.

To permanently set Internet Explorer to ignore these warnings, do the following.

• From the Internet Explorer Tools menu, select Internet Options
• Click on the Advanced tab
• Scroll down to the Security settings
• Check the "Allow active content to run in files on My Computer" option as shown below
• Click on OK and restart Internet Explorer

 Error Messages: What happens if ProMass generates an error message?  Chances are that the error was due to something that is easily remedied. The most common causes of error messages are:

• If you are attempting to process samples from the Xcalibur sample list and your processing method is invalid, you will see the following dialog:

Make sure to check your processing method. Also make sure your processing method scan filter matches the data type (profile, centroid, positive, negative, etc.) that you are trying to process.

• If you are attempting to process samples from the Xcalibur sample list and no chromatographic peaks are detected in the data file the following error message will be displayed:

To fix this problem, open your processing method in the Xcalibur Processing Setup.  Open the raw file that you are attempting to process in Processing Setup.  Check your peak detection parameters and scan filters to make sure that peaks can be detected in your raw file.

• If you tried to process a clipboard spectrum and there was no data on the clipboard, or the data is not in the proper format, the following error is generated:

Make sure you follow the instructions for processing a clipboard spectrum.

• If you don't think your error messages are due to one of the items listed above you can check the ProMass or ZNova error log files. There is a file called ErrorFile.txt which can be found in your ProMass install directory. It keeps a running tab of all fatal errors (i.e., errors that cause either program to terminate without running successfully) generated by either the ProMass GUI or the ZNova algorithm. ZNova also keeps another error log called ZNovaErrors.txt in the ProMass install directory. This file keeps track of any errors produced (fatal or non-fatal) for the latest processing event. This file may be empty, if the last processing event produced no errors. Please feel free to contact us if you cannot resolve the cause of the error messages.
• The following error message may be obtained when trying to open a deconvoluted spectrum in ProMass DecView:

This error message indicates that required Windows scripting components are missing from the PC.  These components are normally installed with Internet Explorer 5.5 or later.  Windows scripting components need to be installed for DecView to work properly.  To download Windows Script for Windows 2000/XP access the following link:

http://www.microsoft.com/downloads/details.aspx?FamilyID=c717d943-7e4b-4622-86eb-95a22b832caa&DisplayLang=en

For Windows NT 4.0 try upgrading to the latest version of Internet Explorer, which should install the script components.

 Xcalibur Sequence will not process :

• On occasion we have seen that a properly configured Xcalibur sample sequence will not process data. When this happens you will see that the Xcalibur Queue Manager reports an empty processing sequence. This is not a ProMass problem. If you have checked that your processing method is ok and that your scan filters match your data type, it could be that your Xcalibur sequence file is corrupted. Copy the sequence rows to the clipboard and paste them into a new Xcalibur sample sequence. Save the new sequence file under a different name, and try reprocessing again. This should fix the problem, if a "tainted" sequence file was the issue.
• If the above did not fix the problem, the Xcalibur processing queue may be hung.  Try exiting and restarting Xcalibur.  If this still does not fix the problem, you may need to manually terminate the Xcalibur processing manager.  Click the Ctrl + Alt + Del keys.  Click the Task Manager button. Click the Processes tab.  Click the Image Name column to sort the processes by name.  Scroll down and look for the processes called queserv.exe and QUEMAN.EXE.   If either of these processes exists, terminate them by selecting them individually with your mouse and then clicking the End Process button.

If you find the need to terminate the Xcalibur processing manager frequently, it is likely that there are problems with your Xcalibur installation or your version of Xcalibur is not compatible with the Windows OS that you are running.  For example Xcalibur 1.3 is only supported on Windows 2000 SP2.  We have seen these problems with Xcalibur 1.3 run on later releases of Windows (e.g., SP3 and SP4).

 BioSequence does not appear in summary report. You have a protein or oligonucleotide sequence in the BioSequence field in your Xcalibur sample list and you are not seeing the sequence or calculated masses in the summary report. What could be the problem? Make sure to enter the kind of sequence (peptide or nucleotide) in the Target Info field, otherwise ProMass will not calculate or show a sequence. Also, when processing your data from the Xcalibur sample list, make sure that you have checked the Replace Sample Info option in the batch reprocess dialog box.

 Blank graphic panes in ProMass web reports.  If you are having trouble with spectra showing up as blank graphic panes, you may want to try changing your image format from PNG to GIF.  The output image format is set from the Results tab of the Build Params screen.  A bug in Internet Explorer sometimes prevents the display of valid PNG files.

 Deconvoluted spectrum does not open in ProMass DecView when double-clicked in the web browser.  See the help topic Viewing Deconvoluted Spectra in ProMass DecView which includes instructions for configuring Firefox to work with DecView.

 Hints For Deconvoluting Noisy Data Sets