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ProMass for Xcalibur Updates
This page contains a description of the latest changes made to the ZNova and ProMass for Xcalibur applications.
The latest full installer package includes ProMass for Xcalibur with ZNova 2.5 SR-1 and was released on 6/15/06. All current users of ProMass for Xcalibur are encouraged to upgrade to this new version. Use the full installer to update a previous installation of ProMass. Check the README for details. Be sure to refer to the guidelines for installing and uninstalling ProMass.
 ProMass Deconvolution 2.5 SR-1, 6/15/06
- Fixed an installer issue with Xcalibur 2.0. Xcalibur 2.0 does not automatically install XDK software components required by ProMass. The new ProMass installer checks which version of Xcalibur is installed and installs the required XDK components if necessary.
- Improvements were made to the ZNova charge state scoring algorithm. A charge series which has a low intensity charge state appearing between 2 high intensity charge states is now penalized in the scoring scheme.
- Added support for IDT's oligonucleotide base notation when specifying a BioSequence in the sample list. To specify an IDT format oligo sequence, enter
sequence = idt
in the Target Info field of the Xcalibur sample list. IDT's scheme for specifying terminal and internal modifications is not currently supported. For more information on IDT's oligo base notation, see:
http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/Default.aspx
ProMass Deconvolution 2.5, 3/14/06:
- Numerous improvements were made to the ProMass DecView application. Both ESI mass spectra and deconvoluted mass spectra are now displayed in DecView. Interactive labeling of charge states in the ESI mass spectra has also been added, which is very useful for validating the results from ProMass. DecView also supports manual calculation of masses by clicking on two adjacent related charge states in the ESI mass spectrum from within DecView.
- Enhancements were made to the ProMass Excel reporting feature. You no longer are required to use the template Excel file. If ProMass does not find a previous Excel report in its results directory, it will create an Excel file called promass_results.xls. The vial # and RT were added to the Excel report columns on the RESULTS sheet. The Excel report now also reports multiple target masses if they are specified in the sample list.
- A new algorithm is used to compute the noise level in the input spectrum. The previous algorithm tended to overestimate the noise baseline and assumed a constant noise level over the entire spectrum. The new algorithm computes the noise level at each data point and is much better at finding low level components with the default S/N threshold setting (S/N threshold = 2). The new algorithm is also more robust when the noise baseline varies considerably. Setting the S/N threshold = 5 will give you results similar to the previous algorithm. Because the threshold is being set lower with the new noise algorithm, ProMass is typically iterating more data points than the previous algorithm. Therefore, you may find that the algorithm takes a bit longer to process a data set, particularly if the noise level is high.
- An improved charge scoring scheme has also been implemented. When charge score normalization is active, scores for candidate masses are normalized based on the number of charge states that are "expected" for a given mass. The "expected" number of charge states vs. mass relationship was derived by inspecting hundreds of experimental spectra of peptides, oligonucleotides, and proteins. The previous score normalization was rather arbitrary and simply normalized the scores based on how many charges were actually detected relative to how many that could be detected over the input mass range. This made the scoring results overly dependent on the input m/z range.
- Savitsky-Golay smoothing is now used for all smoothing operations except those where the smoothing width is > 25 data points. At a setting greater than 25, a simple moving average is used. The default smooth width is now 5. In general, the Savitsky-Golay smoothing method causes much less peak distortion than the simple moving average that was used previously.
- Mass accuracy has been improved for masses determined using non-comprehensive decon mode. Generally, the determined masses will be closer to those determined with comprehensive decon turned on.
- The IgG molecule type has been added to the list of available default parameter sets.
- The "[Raw Data]" link in the ProMass web reports has been renamed to "[View Data]".
- Two new command line options were added to allow setting these ProMass parameters from the sample list. The -y option can be used to turn off comprehensive deconvolution mode (-x turns on comprehensive mode). The -S option can be used to set the S/N threshold, e.g., -S 5 to set the S/N threshold to 5. See the "ZNova Command Line Options Reference" topic in the on-line help for more information.
- The user can now change the default output mass interval to 0.1 Da from the normal 1 Da interval. The option is selected on the Advanced Deconvolution tab in the output mass range settings area of the Build Params screen. The use of a 0.1 Da output mass interval is advantageous when the output mass peakwidths are narrow, as with peptide deconvolution.
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