(1) Parameter Files: What happens if you don't put in a parameter file name in the ZNova Params field of the Xcalibur sequence? ProMass Xcali will use the znova.params file in your install ZNova 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.
(2) Comprehensive 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. Try to limit your deconvolution range to the region of interest when using comprehensive mode, as the algorithm speed is somewhat slower. As it turns out, we tend to use comprehensive mode most of the time for "real world" spectra.
(3) Error Messages: What happens if ProMass Xcali generates an error message? If something bad happens you might see a dialogue indicating "Errors were generated: Contact Novatia Technical Support". Chances are that the error was due to something that is easily remedied. The most common causes of error messages are:
(a) An invalid processing method. Make sure to check your processing method. Also make sure your processing method matches the data type (profile, centroid, positive, negative, etc.) for the data type that you are trying to process.
(b) You tried to process a clipboard spectrum and there was no data on the clipboard. Make sure you follow these 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 ProMassXcali 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 ProMassXcali GUI or the ZNova algorithm. ZNova also keeps another error log called ZNovaErrors.txt in the ProMassXcali 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.
(4) 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 Que Manager reports an empty processing sequence. This is not a ProMass problem. If you have checked that your processing method is ok, 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 problem.
(5) 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 calcuated 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 as described here, 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 dialogue box.
