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ProMass for Xcalibur Previous Updates
To find out what version of ProMass you are running, open the ProMass for Xcalibur homepage and access the Help|About ProMass ... menu. The version number is displayed in the dialogue. Versions prior to 1.2.3 do not have the About menu. In this case, go to your ProMass install directory. Locate the ProMassXcali.exe file. Right click the file to access the Properties window. Click on the Version tab. The latest version is 2.5 SR-1.
ProMass Deconvolution 2.3, 3/14/05:
- A new feature was added that allows the deconvoluted spectra to be
viewed by double-clicking the graphic pane in the ProMass web report.
The viewer is called ProMass DecView, which can be used to view any
ProMass deconvoluted spectrum output (.dec) files. ProMass DecView is
also available from the ProMass HomePage under the new Tools menu. In
order for ProMass DecView to work from the web browser, the browser
must support ActiveX controls. This limits use to Internet Explorer
for this feature. However, clicking on the "Raw Data" link will also
allow you to open the data into the viewer from any browser, even those
that do not support ActiveX. You must configure your browser to open
the .dec file instead of downloading or saving it to your system.
- ProMass can now output its graphic images in GIF format.
This was added due to Internet Explorer's inability to display certain
ProMass image files in PNG format. This is a bug in IE, not ProMass.
If you are having trouble with many of your spectra showing up as blank
panes, you may want to try the GIF format instead. The output image
format is set from the Results tab of the Build Params screen.
- The help system was updated with the new changes
incorporated since v. 2.0. Online help is also available for the new
ProMass DecView application.
ProMass Deconvolution 2.2, 1/31/05:
- Fixed a problem with the license key algorithm which was not working properly for some international customers. The license validation screen was improved with the addition of copy/paste and browser buttons for the license keys. Also, instructions were changed to point demo users to Thermo's website.
- Fixed a problem in the Browse ProMass Files... menu item on the ProMass HomePage. Sorting the file list by date did not work properly and has been fixed.
- ProMass now supports automatic background subtraction in automated mode (i.e., when run from the Xcalibur sample list). To activate background subtraction, open your processing method and select the "Spectrum Enhancement" tab. Click the "Enable" check box. Select the "Combine" option and choose your settings. Save your proc method. Note that "Combine" is the only spectrum enhancement method currently supported. To turn off spectrum enhancement, uncheck the "Enable" option in the processing method and save it.
- A menu item called "Settings" was added to the ProMass HomePage. From "Settings" you can choose to hide the ProMass console if desired. You may find this useful during automatic processing if you want to avoid having the console constantly pop up while you are trying to perform other Windows tasks.
- Also, from the ProMass HomePage Settings, you can choose a ProMass task priority. Generally, you should set this to "Normal". Setting the task priority to "Low" may be useful if you want to automatically process data while acquiring data and want to prevent ProMass from consuming excessive system resources.
- ProMass now displays results in your default web browser. Previously, ProMass always launched results in Internet Explorer, regardless of the default browser setting.
- For automated runs initiated from the Xcalibur sample list: The Client field is now included in the chromatogram-level summary, if it has been entered in the sample list. The Processing Method is now logged in the log file. Automatic updating of automated processing results in Internet Explorer has been disabled. Due to a bug in Internet Explorer, this feature was not working reliably on many systems. This means you will need to hit your browser refresh button to the see updated ProMass results from automated sample list processing.
- An Excel template has been included with the installer that allows you to plot a ProMass decon spectrum (.dec file) in Excel. The Excel template is called "promass_spectrum_template.xls" and can be found in the ProMassXcali\Excel directory.
ProMass Deconvolution 2.0 SR-1, 6/15/04:
- This was a maintenence release to correct an installer issue. The ProMass installer was changed to include certain Windows-specific files that are missing on some installations of Windows. If the file(s) were not previously installed on the Windows machine, the Build Params screen would not load properly and generated an error message indicating certain windows files were either missing or not properly registered. This has been fixed with this and later versions of the installer.
Version 2.0, 4/20/04
- This marks the initial release of ProMass for Xcalibur by Thermo Electron.
- Changed to a new installer, which installs ProMass for all
users instead of just the current user logged in. A PDF user's guide
and updated help files are installed with the new user manual and are
accessible from the Windows start menu.
- ProMass now recognizes the .params file
format. Double-clicking on aZNovaparameter file will automatically
open that parameter file in the Build ZNova Params dialog.
- Added the capability to specify the results directory using
the command line option -D. This feature is useful for setting the
ProMass output directory directly from the Xcalibur sample list in the
ZNova Params field. The syntax for specifying the output directory is
-D followed by a double-quoted string for the directory path, e.g.:
-D "C:\data\promass"
- Added a new feature that allows the user to produce a sequence ladder summary
in the chromatogram report. This feature can be used to search for
oligonucleotide sequence failure products, exonuclease digestion
products, or N or C-terminal processing of proteins. See the help
topic on "Producing a Sequence Ladder Summary".
- Added the capability to automatically delete all
non-essential files after ProMass processing is completed. The option
is a checkbox on the Results tab of the Build ZNova Params dialog.
This will delete Xcalibur results files (.RST) and the ProMass input
text files (.txt). When processing large numbers of data files,
automatically deleting these files can save significant disk space.
Version 1.4.6, 2/2/04
- Added a feature to report %Total abundance of the target masses in the report.
- Added %Total and %Relative abundance to the deconvolution peak report.
- Fixed an intermittent problem where UV or MS chromatogram would not be plotted.
- Improved peak labeling in Data Points labeling mode.
- Changed status color logic to allow for green status when 2
target masses were found in the same spectrum. Previously, this would
yield a purple or yellow status as the 2nd component would be treated
as a contaminant.
- Changed the help system from windows-style to the new HTML Help.
- Added protein LC/MS example data and sample list in the TestData/protein lcms directory.
- ProMass Xcali is now called "ProMass for Xcalibur" in documents and installation dialogs.
Version 1.4.3, 4/13/03
- Changed configuration file znova_masses.txt to an ini file format (znova_masses.ini)
- Added a link to the raw data points in the HTML report.
The feature is accessible from the either the Deconvolution or Zoom
Deconvolution section and is labeled [Raw Data].
- Improved the deconvoluted spectrum labeling features.
You can now specify whether to label mass peaks as raw data points or
components. You can also specify a spectrum label relative
intensity threshold. The options can be set from the Build Params
screen from the Results tab.
- Fixed a bug related to parameter file entry in the Xcalibur
sample list. If the parameter file name or path contained a "-"
character, the file would not be read.
- Fixed a bug related to normalization of the spectum and
chromatogram graphs. In certain cases, graphs were not being
y-normalized within the x axis limits.
Version 1.4.1, 12/12/02
- Added capability to calculate masses of RNA sequences. Use
'sequence = rna' (without quotes) in the Target Info field of the
Xcalibur sample list to invoke calculation of RNA sequences in ProMass
processing.
- A separate set of RNA residues was added to the znova_masses.txt configuration file to support RNA mass calculation.
- Fixed a problem with importing and processing of spectra copied from Bioworks Browser to the clipboard.
Version 1.4.0, 11/12/02
- Added a new Excel summary feature. The Excel summary
provides a concise summary of results similar to the ProMass
Browser. It's a convenient way to integrate sample
submission (from a client or collaborator) and reporting. See the
help topic "Using the Excel Summary Reporting Feature" for more
details.
- Added a new feature which performs auto target mass
deconvolution scanning. If you leave the output mass range fields
blank in your ZNova parameter file, the output decon range will
automatically default to +/- 25% of your target mass range.
- Changed the Mass Error field in the chromatogram summary to indicate Da as well as %.
- Added "hover text" to the ProMass browser summary page.
If you hover your mouse over a sample well it will indicate the base
peak mass for that sample. If you hover your mouse over a target
mass in the ProMass browser, the observed mass that matches the target
mass will be displayed.
- Improved labeling of peaks in the graphical spectrum display.
- Changed the explicit target mass feature so that you can
specify masses in the Target Info field as comma or space separated
values, e.g., 1000, 2000, 3000. The old syntax was:
targets = (1000, 2000, 3000)
The old syntax still works, but just seemed too cumbersome. See the
help topic Configuring ProMass to Search for Target Masses for more
details.
- Added feature to allow a protein or oligo sequence file to
be specified in the BioSequence field in the Xcalibur sample list. This
feature is particularly useful if your BioSequence string is beyond the
255 character limit imposed by the Xcalibur sample list. See the
help topic "Automatically Calculating Masses of Biomolecules" for more
details.
- Added additional menu items on the ProMass Xcali home page which allow convenient location and browsing of ProMass results.
Version 1.3.0, 7/31/02
- An optional color-coded sample plate (e.g., 96-well) viewer was added to the ProMass summary page. Here's an example.
- The GUI on the Build ZNova Params screen was revamped to a tabbed dialogue to improve ease of use.
- Some of the parameters were moved from the znova_masses.txt
configuration file to the standard ZNova params file. The necessary
controls were addedto set these parameters in the Build
ZNova Params dialogue. The znova_masses.txt file still exists but is
only used for configuring custom masses of amino acids, nucleotides,
and termini. Note: if you want to use one of your existing
parameter files make sure to open it in the Build Params screen and
save it again, so that your parameter file will be updated with the new
options.
- The name of the "Exhaustive Deconvolution" parameter was
changed to "Comprehensive Deconvolution". It sounds a little less
scary.
- The operation of ZNova-ize sequence was changed so
that you no longer have to hold down the control key to add parameters
to the Xcalibur sequence.
- The name of the "Novatia" parameter field in the Xcalibur
sample list was changed to "Target Info". Operation is otherwise the
same.
- Context-sensitive windows help was integrated with the program.
Version 1.2.4, 5/13/02
- Fixed a minor problem with ZNova which caused the smoothing
operation to be slow in certain instances. Added a feature which
allows the baseline removal factor to be specified as a parameter string or command line argument (-b).
Version 1.2.3, 3/19/02
- Added a new option called raw to the Directory Format parameter on the Build Params screen. The raw option allows you to have your deconvolution output files automatically saved in the data file path. This option is now the default way
output files are saved. A subdirectory is created in the data path called promass_results that contains all of the output files. This option prevents you from having to worry about setting up a Results Directory prior to processing your files.
- Added a File | About... menu entry to the ProMass Xcali home page to allow for a simpler method of checking the program version number.
Version1.2.0, 2/04/02
- The ProMass Browser button was enabled on the ProMassXcali home
page. Clicking on this button opens the latest top-level summary
page inan Internet Explorer browser window. This prevents
you having to search your hard drive for the last processing result.
Version 1.0.0.244, 12/06/01
Version 1.0.0.243, 10/09/01
- A new feature was added to the Build Params screen to assist the user in parameter file creation. When you hit the Default Params button, you can now select a default parameter file that is appropriate for many different applications (e.g., peptide, oligonucleotide, small protein, large protein).
Version 1.0.0.162, 9/25/01
- Added the capability to process a clipboard spectrum within the Build Znova Params
screen. Set up your parameters, paste your Xcalibur spectrum to the
clipboard, and hit the clipboard button. The spectrum will be processed
with the current set of parameters. When done, ProMass Xcali will
launch an IE window to display the results. Please note: copying
profile spectra to the clipboard can be a very slow process. This is an
Xcalibur "feature".
Version 1.0.0.153, 9/23/01
- This update is installed as a patch on top of 9/14/01 full
installation. Fixed problem with summing a large number of centroid
scans. Previously, if more than 30 centroid scans were summed with
high intensity ( >10 E+9) a data overflow fatal error may have been
observed. This has been fixed.
Version 1.0.0.124, 9/14/01
- Cleaned up installation program by employing Visual Studio Installer.
Version 1.0.0.103, 8/31/01
- Added link to ProMass Xcali web documentation from the help menus of Build Params File and ZNova-ize Sequence. Only tested with internet explorer.
- Added help text features within the Build Params File and ZNova-ize Sequence programs. Move your mouse over the parameters and help text is displayed at the bottom of the window in a status area.
ZNova Previous Updates:
To find out what version of ZNova you are running, go to your
ProMass Xcali install directory. Go to the ZNova subdirectory. Locate
the xznova.exe file. Right click the file to access the Properties
window. Click on the Version tab.
ZNova Version 1.2.2 2/16/02
- Fixed a minor problem with the displaying of the raw ESI mass
spectra. If you had either Centroid Plot turned on or smoothing
turned off, your input ESI spectrum would not be displayed properly in
the output. This had no effect ondeconvolution results.
Version 1.2.1 2/12/02
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The ZNova algorithm in version 1.2.1 was further optimized vs. 1.2.0 by using ActiveState's new version of PerlApp.
Version 1.2.0 2/04/02
- The ZNova core algorithm has been optimized which has produced a
significant increase in speed (up to 10X) for certain
applications. Get the full details here.
Version 1.1.5 12/05/01
- Fixed a problem with automatic launching of the top-level summary
in Internet Explorer on NT in ZNova 1.1.3. This error caused
ZNova to hang without finishing on some systems. The
"hang"has been fixed. The auto-launching feature does not
work on NT due to a Microsoft issue. The feature does work on Windows
2000. NT users have to manually navigate to the summary
page which is found in the base results directory.
Version 1.1.3 12/03/01
Version 1.0.0.21 10/24/01
- A feature was added to the text-based Deconvolution Peak Report
output to show Delta Mass from the base peak in the deconvoluted
spectrum. Also, the centroiding and peak labeling of exhaustive mode data was improved.
Version 1.0.0.18 9/28/01
- Fixed the interpolation problem which was present in the 1.0.0.17
release. You can now acquire centroid data and have the output as
profile with very good results.
Version 1.0.0.17 9/25/01
- Fixed a problem that was occurring when processing low charge state
spectra (e.g., peptides). Charge state of "1" was not being properly
assigned, when singly charged ions were only ions present
- KNOWN ISSUE: Interpolation of centroid data
to profile data still needs work. Absolute intensities may be too high
by a factor of ~2 if centroid data are processed and the Centroid Plot box is unchecked. Until this is addressed, we recommend that you check the Centroid Plot box when processing centroid data (note: fixed in 1.0.0.18).
Version 1.0.0.16 9/23/01
- This update is installed as a patch on top of 9/14/01 full installation.
- Added capability to offset UV or Analog detector chromatographic peak labeling via the znova_masses.txt configuration file.
- Fixed problem that occurred when profile data with m/z step
size gt; 0.1 u was analyzed. Now data are interpolated to 0.1 u if
step size is larger than 0.1.
- Added capability to plot profile deconvolution even when
centroid data are used for input. This is accomplished with the new
input data interpolation routine. Previously, centroid input spectra
always yielded centroid output spectra. The plotting of centroid output
is now determined by the Centroid Plot ZNova parameter.
- Added capability to read Macintosh-based mass-intensity text files without conversion.
Version 1.0.0.14 9/14/01
- Updated ZNova to be compatible with the new installer.
Version 1.0.0.13, 8/29/01
- Changed the way residue masses for nucleotides were added. The
residue masses of the nucleotides contain terminal O, and HPO3.
Oligonucleotide sequences do not contain terminal phosphate groups by
default. If you do not specify termini, H and OH will be added as
termini, resulting in terminal OH groups at the 5' and 3' ends.
Therefore, if your oligos contain a phosphate group you need to add a
terminal phosphate using the termini option, e.g., put termini = H, POH in the Novatia field of your Xcalibur sample list.
Version 1.0.0.12, 8/28/01
- Made a few minor changes to the program syntax for readability, does not affect program execution in any way
Version 1.0.0.11, 8/25/01
- Fixed a problem with xznova.exe. If a parameter filename started
with a number and/or contained a hyphen, the parameter file would not
be read in correctly resulting in an error.
- Fixed a problem with a xznova.exe. The BioSequence string
from the Xcalibur sequence was displayed in the html report as one long
string, therefore, for a very long sequence, the string could run off
the edge of a page. Added html line breaks after every 50 residues and
added markers to indicate residue position.
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