ProMass for Xcalibur release notes

Current Release: ProMass STD/HR for Xcalibur, ver. 4.0 rev. 2, build 01.05.23

• This is a maintenance release to fix a few minor issues.
• Added code to prevent duplicate values for residue definitions in mass definition file (znova_masses.ini). If a duplicate residue definition is found, the value for the first instance of the definition is used and a warning is logged to the error file.
• Fixed an issue with ZNova charge deconvolution when processing LCMS data with multiple chromoatogram peaks. Excessive noise filterning of spectra could occur in rare cases. This did not affect data using PPL deisotoping or PPL charge deconvolution methods.
• Previously only oligo residues using the bases ACTGUI preceded by lower case (m, r, f, x) or + were recognized (e.g., mA, rA, fA, xA, +A). Base definitions preceded by lower case (a-z) or + are now supported, which allows the user to create more custom oligo residue definitions.
• The ProMass installer now includes the Sentinel run time libraries, which allows the license key to authenticate over Windows remote desktop. Please note the license key does not allow remote and locally connected users to process data simultaneously. If the license key detects more than one concurrent user, an error message is displayed.

ProMass STD/HR for Xcalibur, ver. 4.0 rev. 1, build 07.17.20

• ProMass branding and graphics have been updated to a cool new look!
• ProMass can now automatically calculate drug-antibody-ratio (DAR) and display the results in the ProMass report. Includes support for multiple target masses, subunits, and drug masses.  See the ProMass help pages on how to use this handy new automatic DAR calculation feature!
• The on-line help pages and PDF User Guide have been vastly improved and updated.
• Added new “send spectrum to PPL ReView” function to ProMass HR to allow easier exporting of data to ReView for building PPL methods.
• Corrected problem with purity calculations when depurination peaks were set to be ignored in the znova_masses.ini file.
• Added the ability to print reports to PDF. This option is selected from the ProMass parameters editor (Build Params) on the Results tab under the Graphics options. This option prints samples reports in both PDF and HTML. The PDF reports are stored in the same results folder as the HTML reports.
• Previously, the purity estimate was not corrected for an adduct which was found as the base peak with a target mass found as a minor peak. This has been changed to allow purity correction even when an adduct is the base peak.
• Fixed Excel reporting compatibility with Office 365.
• You can now copy a ProMass parameter file command string from Build Params and paste it into the sample list.
• Added new “Reset Xcalibur Batch Processing Parameters” function to the ProMass Tools menu. This can be use to put Xcalibur back to Qual processing mode.

ProMass STD/HR for Xcalibur, ver. 3.0 rev. 12, build 03.22.18

• A new in-line DecView feature was added. When you click on a [View Data] link or double-click a spectrum pane, a new in-line interactive spectrum viewer is launched within the web browser.  This allows you to execute many of the same functions of DecView directly within the browser.  DecView is still available for those users who prefer the features of the DecView windows program.  A Show Help button is available within the in-line DecView pages that describes how to use these pages.
• This version of ProMass was modified to be compatible with Xcalibur 4.1.  Xcalibur 4.1 does not update the results (.RST) file when processing data from the sample list, even when the Replace Sample Info option is selected. ProMass was updated to pull this information from the sample list (sequence file) instead of the results file.
• Note for Xcalibur 4.1 and later: These versions of Xcalibur contain a bug which causes the error message “Calibration file not specified” to appear when a user attempts to perform qualitative processing. Click this text to download a folder containing instructions in a Word document as well as an executable file to resolve the issue.

ProMass STD/HR for Xcalibur, ver. 3.0 rev. 11, build 09.28.17

• Fixed plotting of chromatograms where peaks were not being labeled properly in some cases.
• ProMass now allows automatic processing of MS^n data. Be sure to select an appropriate scan filter for the scan type you want to process in your Xcalibur processing method. There is no capability at this time to process all MS^n scans, only what is defined by the scan filter in the proc method.
• The -L command line option has been updated to allow for multiplier values.  For example, if the command “-L 2M” (without quotes) is entered in the ZNova Params field of the sample list, the maximum deconvoluted mass will be set to twice the maximum target mass.  Floating point values are also allowed, e.g., “-L 2.5M”.  Note there cannot be a space between the multiplier value and the letter “M” in the command.
• Fixed an issue where Thermo Ultimate autosampler vial locations were not being mapped properly to the plate view.
• The way ProMass handles the deconvoluted mass range has been changed slightly, when auto processing from the sample list. Previously, if no mass range was defined in the ProMass parameter file or with a command line option (e.g., -F or -L), ProMass would use an output deconvoluted mass range equal to +/- 25% range around the target mass(es). The new change uses a minimum deconvoluted mass equal to the lowest input m/z.  The default maximum deconvolted mass is still the largest target mass +25%.
• Setting the output mass range for PPL charge deconvolution or deisotoping will truncate the PPL results to the mass range in the ProMass method. This does not change the PPL method in any way.  It only serves to truncate the output range if it is beyond the set limits in the ProMass parameter file.
• Fixed sequence ladder summary with regard to calculation of oligo sequence ladders containing phosphorothioate residues.
• Added two new auto processing report templates: auto_proc_total_peak_summary.html, and auto_proc_inline_peak_table.html.  The total peak summary report includes a total deconvolution peak report summary at the bottom of the report.  The table is sortable by mass, intensity, RT, or identity. The inline peak table report includes an inline peak report table after each deconvoluted spectrum.

ProMass STD/HR for Xcalibur, ver. 3.0 rev. 10, build 12.12.2016

• Included intensity as another reported field on the main automatic summary report page. The intensities are now shown for all target masses, or the base peak intensity if no target mass is provided. This applies to automated processing only.
• The deconvolution program executable (xznova.exe) is now 64-bit, which improves speed ~20% in some applications.

ProMass STD/HR for Xcalibur, ver. 3.0 rev. 9, build 4.26.2016

• Fixed Excel report compatibility with Excel 2013.
• Added a new directory format called “tray”. When this option is selected, the ProMass results will be directed to a folder named after the autosampler tray. This is useful if you wish to acquire multiple trays worth of data into a single acquisition directory. For example, if your tray is named “CStk1-01”, the results directory would be named “CStk1-01_results”.
• Fixed an issue where the cumulative purity was not being reported correctly. In certain cases, a single impurity greater than the relative intensity threshold and less than the cumulative purity threshold would still trigger a purple status when cumulative purity was selected.
• You can now enter ladder=impurities in the Target Info field of the sample list to list the found impurities in the Sequence Ladder Summary.
• Fixed an issue in the ProMass application where the PPL tab would not be shown when a parameter file was opened directly by double-clicking the parameter file.
• Included mass tolerance and minimum tolerance in color coded key at the botttom of the report pages.

ProMass STD/HR for Xcalibur, ver. 3.0 rev. 8, build 9.15.2015

• Added a feature to use the mass tolerance from the processing method when averaging spectra in ProMass. This was done because Xcalibur does not always add spectra correctly when processing data automatically unless a mass tolerance is specified. For Orbitrap data, the mass tolerance in the Processing method should usually be set to 1-10 ppm. 5 ppm is a good general setting for Orbitrap use at 30k resolution. The tolerance should be tighter for higher resolution data. For other, non-accurate mass instruments, the default 500 mmu setting should be used.
• This release is the first release to support the Safenet Sentinel hardware key.

ProMass HR for Xcalibur, ver. 3.0 rev. 7 preview release, build 04.30.2014

• The resolution enhancement feature “PPL peak deconvolution followed by ProMass deconvolution” was not working properly and was fixed.
• A translate sequence feature was added. This is an advanced feature, but it allows the user to write a perl program called translate_sequence.pl that will translate a user oligo or protein sequence and translate it to a sequence format that ProMass understands. The feature requires the perl program translate_sequence.pl to be present in the installation ZNova directory (typically, C:\Program Files\ProMassXcali\ZNova). The perl program must be called exactly ‘translate_sequence.pl’. See the example_translate_sequence.pl file for an example of how this works.
• Added the “Integrate Intensities” option. This instructs ProMass to sum mass spectra instead of average. The deconvolution results are more quantitative when this option is used.
• Added an option to specify a custom mass configuration file. Normally, ProMass uses the znova_masses.ini file in the installation\ZNova directory. Currently, the option is only available from the command line using the -Z command. The usage syntax is, e.g.:
  -Z “C:\myfiles\custom_masses.ini”
  As you can see from the above, you must use a double quoted string encompassing the full path and file name of the custom masses file.
• The ProMass and PPL ReView software have been combined into a single installer to make it easier to install.

ProMass HR for Xcalibur, ver. 3.0 rev. 5 preview release, build 07.25.2013

• Added capability to run an external program after processing with the ñr option. To use this feature, specify the -r option in the ZNova Params Xcalibur sample list field, for example:-r “C:\myprogram\example.exe arguments”The command should include double quotes around the program and any optional arguments for running the program.
• Added the ability to specify a modified residue using definitions within brackets [] in addition to the normal forward slashes //. For example, [mod] = 100.1 is the same as /mod/ = 100.1 in the znova_masses.ini file.

ProMass HR for Xcalibur, ver. 3.0 rev. 2 preview release, build 05.13.2012

• This is the initial release of ProMass HR for Xcalibur. ProMass HR is a special version of ProMass that includes the tools from Positive Probability, Ltd. (PPL) to allow high resolution (exact mass) deisotoping. Any method created within PPL can be automated through the ProMass HR interface.
• Added capability to perform ProMass charge deconvolution on PPL peak deconvoluted spectra.
• Improved the “Label All Peaks” feature in ProMass DecView.
• Fixed a bug regarding the Deconvoluted Spectrum Labeling threshold and the calculation of spectral total abundance. The total abundance of deconvoluted ions was not being recalculated after applying the threshold for PPL-processed spectra.

Changes in ProMass v. 2.8.5, ZNova v. 3.0.2, build 07.28.2014

• Added the ability to specify a modified residue using definitions within brackets [ ] in addition to the normal forward slashes / /. For example, [mod] = 100.1 is the same as /mod/ = 100.1 in the znova_masses.ini file.
• Increased the maximum input mass range from m/z 6000 to m/z 20,000 to allow for use on Oribtrap EMR instruments. Output deconvoluted mass range maximum has been increased to 5E+6.
• Added the “Integrate Intensities” option. This instructs ProMass to sum mass spectra instead of average. The deconvolution results are more quantitative when this option is used. This change only affects data automatically processed from the sample list.
• Added the capability of entering offset output mass ranges in the ProMass parameter file from the Build Params utility. This feature is only useful when running in automated deconvolution mode from the Xcalibur sample list. For example, entering -5000 in the minimum output mass box will set the lowest deconvoluted mass to 5000 Da lower than the lowest target mass. Conversely, setting the maximum output mass to +5000 will set the highest deconvoluted mass to 5000 Da higher than the highest target mass.

Changes in ProMass v. 2.8.2, build 04.10.2012

• ProMass 2.8.2 was built on Windows XP with Xcalibur 2.0.7.  If you have an earlier version of Xcalibur, use the standard release of ProMass 2.8.  ProMass 2.8.2 has been tested to work fine with later versions of Xcalibur (2.0.7 – 2.2) and Windows 7 32-bit and 64-bit versions.
• Fixed a problem with processing data where Agilent UV or PDA detectors were in use.  In automated mode, ProMass would not autoprocess data with an Agilent detector configured.
• ProMass is a 32-bit application, however, it does work on Windows 7 64-bit versions. It is recommended that you install ProMass in the win32 default directory, which is: C:\Program Files\ProMassXcali.  On 64bit windows, the installation program will automatically install ProMass in C:\Program Files (x86)\ProMassXcali unless this is changed in the ProMass installation dialog.  By changing the installation directory back to the default win32 location, all of the test data will process without having to update these files to a different installation directory.

Changes in ProMass v. 2.8, build 12.4.2010

• The old DNA and RNA sequence types have been removed – it was just too confusing to have multiple types of oligo sequences. Now there is only one oligo sequence type, which behaves like the previous IDT sequence type and supports many different types of oligo residues.  As a result, the format of the znova_masses.ini file has been changed significantly.  If you have made additions to your znova_masses.ini file, you will have to re-enter them at the appropriate locations in the new znova_massies.ini file.  The ProMass installer will make a backup of your original file and save it as znova_masses.ini.bak in case you need to copy your custom definitions into the new file.  Specifying ‘sequence=oligo’ (without quotes) in the Target Info field of the sample list will indicate an oligo sequence.  The statement ‘sequence=idt’ also still works.
• ProMass now supports entering multiple sequences (e.g., oligo duplexes) in the BioSequence field of the sample list. Two or more sequences are entered by separating them with commas, e.g.,:

ACTGACTGACTG, GCATGCATGCAT

Sequence ladders will be calculated (if specified) on each individual sequence strand.  There is no limit to the number of sequences that you can enter, but the Xcalibur BioSequence field has a limit of 255 characters.

• ProMass will calculate a duplex target mass from two oligo sequences by entering ‘sequence=duplex’ (without quotes) in the Target Info field of the sample list.  ProMass will add another target mass to the list that is the sum of the masses of the 2 sequences.  Currently, there is no way to calculate ladders from duplexes.  Ladders (if specified) are calculated based on the 2 individual strands, since oligo duplexes generally dissociate into the individual strands when electrosprayed.  If more than one duplex needs to be entered, enter the sequences in order (1,2,3,4), because ProMass will add them 2 at a time in the order that they are entered (1-2, 3-4, etc).
• The merge width parameter has been changed so that merge width can be set to give a more accurate centroid without affecting the ZNova score.
• A feature was added to turn off reporting of terminal phosphate matches from the sequence ladder report.  Enter ‘termini=no phos’ (without quotes) in the Target Info field to disable terminal phos matches in the sequence ladder summary.
• New logic has been applied to the assignments of ladder sequence searches.  The new logic removes coincidence matches of ladder sequence candidates that appear to be adducts.  For example, each subsequence that is found is evaluated whether it could be an adduct (e.g., Na) of another subsequence.  The logic applied is that if a component that is in the same chromatographic peak as the non-adduct (parent) and the candidate intensity is less than the parent peak, then it is assumed that the candidate is indeed an adduct and not a different ladder sequence from the parent peak. The caveat is that this new logic could lead to an occasional false negative if the chromatographic separation is poor.  However, testing revealed that this scenario is a lot less likely to happen versus the false positve matches that were being generated without the new logic.
• Mass definitions in znova_masses.ini file are now case-insensitive.  Previously, ‘/5Phos/’ and ‘/5phos/’ were two different things.  Now, they are considered the same thing.
• Average masses (centroided values) are now reported as the intensity weighted mean of the charge series instead of the arithmetic mean that was previously reported.
• A ladder mass list CSV file is automatically created and saved in the promass results directory when ladder sequence searching is enabled.  The CSV file lists all possible ladder sequence masses, where the ladder masses listed in the ProMass report are only those that were found.
• A handy new “popup view” feature has been added to the top-level summary report (index.html) file when performing automated analysis.  Clicking on the ‘Popup View’ link on the main summary page will display a separate browser window for viewing the 96-well plate and sample list.  Mouse clicks in the pop-up view are directed back to the main display, which allows you to very rapidly scan through a 96-well plate without having to keep going back to the main page.
• ProMass now allows for cumulative impurity thresholds when reporting target masses during automatic processing.  Previously a “green” status sample could be demoted to “purple” only if one or more peaks exceeded the relative intensity threshold value.  When the new Cumulative option is selected, the sum of all impurities is included.  For example, with the Cumulative option checked the appearance of 3 impurities at the 11% level can trigger the “purple” status with a threshold setting of 30%, since the sum of the 3 impurities is greater than the threshold setting.
• Added two different auto processing threshold parameters (Chrom Peak Selection Thresholds).  These are most useful for LC/MS processing when you want to limit selection of chromatographic peaks for deconvolution below a selected threshold.  The MS Intensity processing threshold limits the selection of peaks based on the base peak intensity at the peak apex of each chromatographic peak.  The area % threshold limits chromatographic peaks by their integrated peak area %. The auto processing thresholds are set from the Reporting tab of the Build ZNova Params utility.
• ProMass reports are now produced by populating template html files.  Three report templates are used, which are stored in the ProMass templates directory:
  • summary.html – this template is used to generate the top-level ProMass browser summary used during auto processing
  • auto_proc.html – this template is used to generate the sample-level report used during auto processing
  • manual_proc.html – this template is used to generate the manual processing report
• The advantage of the templates is that it is possible for the user to modify the templates to change the look or information content contained in the reports.  Some additional examples are provided in the ProMass templates directory.  This is mainly considered a “power user” feature at this point.  It is suggested that you contact Novatia if you have specific reporting requirements and need help configuring custom templates. The template files are specified on in the Report Templates section on the Results tab of the Build Params parameter setup utility.
• All fields on the Results tab of the parameter setup utility now require a double-click to select a file or directory.
• ProMass now automatically writes an XML summary file during automatic processing.  The file is called promass_results.xml and is written to the results directory.  The XML file contains all the relevant information about each sample processed from the Xcalibur sample list. The XML output is one method that can be used to import ProMass results into a database. An annotated XML file is included with the installation in the ProMass install directory.  See the file called promass_annotated.xml.
• ProMass DecView 1.3 is included which has a handy new “Track with Label Click” feature for relative mass labeling and improved handling of manual and auto peak labeling.
• Previously, ProMass could only calculate a sequence ladder that contained one of the termini.  ProMass can now calculate all possible internal fragments when producing a sequence ladder summary.  For more information see the “Producing a Sequence Ladder Summary” help topic under “ProMass Reference” in the on-line help.
• Some changes have been made to the ProMass web report templates.  All columns in the ProMass web report tables are now sortable by clicking on a table heading.  Clicking on a table heading again will reverse the sort.  In the manual report template, the deconvolution peak report is now a sortable table at the end of the report instead of a link to an external text file.
• Instructions were added to the on-line help for configuring Firefox to automatically open ProMass DecView files.  See the help topic “Viewing Deconvoluted Spectra in ProMass DecView” for more information.
• Fixed a rounding error in the reporting of purity estimates in the ProMass automated report.

Changes in ProMass v. 2.7

• Added support for PTM (post translational modification) searching. When proteins are expressed in real biological systems, the masses of target proteins may not be known exactly, as a result of post-translational modifications (PTMs).  Conveniently, ProMass can be configured to automatically search for user-defined PTMs for each target mass that is defined. PTM targets are different than normal ProMass target masses in that they are only displayed in the ProMass reports if they are found.  PTM masses are defined in the znova_masses.ini file as mass differences from target masses.  Putative PTMs are automatically listed in the Target Mass summary of the ProMass report and on the Excel summary sheet if it is utilized.  See the on-line help topic “Automatic Identification of PTMs” for additional information.
• A new field, Presumed Identity, was added to the Excel summary to provide more information when PTM searching is utilized.  When a PTM is found, its identity is indicated in the Presumed Identity column.  Otherwise, the Presumed identity will indicate “Target Mass” or “Not Found”.
• The top 5 mass display in the Excel summary is now linked to the “Report When Target Mass Not Found” setting in the ZNova parameter file.  When set to “Base Peak” or “None”, the Excel summary will indicate the top 5 highest intensity masses found.  If set to “Closest Mass” Excel will report the 5 closest masses to the target mass.
• Added a new setting on the ProMass Home Page – Show or Hide Error Messages.  With Error Messages setting set to “Show” (default), when ProMass encounters an error that prevents processing of a sample, a dialog prompt is displayed, temporarily halting processing of the data until the user clicks on the OK button within the dialog box.  Alternatively, the “Hide” setting will instruct ProMass to log the error and to continue processing the remaining samples in the list.  Any errors that have been logged can be reviewed by accessing the “Tools | Error Logs | View” menu item from the ProMass Home Page.

Changes in ProMass v. 2.6, build 09.11.2006

• Fixed a problem with the -D ZNova Params option which specifies an explicit results directory. The -D option was not working properly if the -P option was also specified as a parameter string in the sample list.
• Fixed a problem which caused PDA chromatograms to not be displayed in the ProMass web-based reports.
• Some systems were prone to automation errors upon upgrading to Xcalibur 2.0.  The errors occur when ProMass attempts to export chromatogram data from the raw file.  This is believed to be due to the use of instrument methods from older versions of Xcalibur.  The safest thing to do is to recreate new instrument methods on Xcalibur 2.0.  This version of ProMass ignores these errors as a work around.
• Completed full support for IDT’s base notation format, including support for internal and terminal mods.  Modifications and terminal groups are entered in the BioSequence string between slashes, e.g., /mod/.
• Added support for defining user residues in the sample list.  This allows you to define custom groups in the sample list without having to define them in the znova_masses.ini file.  For example, your BioSequence string could contain the string: ACTG/mod/GATAC.  In the Target Info field of the sample list you would give the MW of the mod like this: /mod/=305.3, which would indicate that the modification defined by /mod/ has a mass of 305.3.
• ProMass can now automatically report the presence of impurities, contaminants, or degradants in deconvoluted spectra.  Any component which is not a target mass is a putative impurity, contaminant, or degradant.  Species including known cation or solvent adducts, and labile functional groups can be included in the automatic assignment.  The automatically assigned components are listed in the Presumed Identity column of the Deconvolution Peak Report, which is available from the [Deconvolution Peak Report] hyperlink in the ProMass report for each sample. In order for ProMass to automatically assign known impurities, contaminants, or degradants, the following conditions must be met: (1) ProMass must be run in automated mode from the Xcalibur sample list. (2) At least one target mass must be specified in the sample list, either explicitly, or by including a BioSequence string and sequence type definition. (3) Masses for known impurities must be configured in the znova_masses.ini configuration file.  Several common impurities and contaminants have already been defined for you, but it is simple to add new ones by editing this file with Notepad.  (4) User residues, which are defined in the Target Info field of the sample list using the /mod/ = mass format, are automatically searched for as potential known components.  The existence of plus and minus the user-defined mass are searched for as known components.
• Added a Minimum Intensity parameter. In order for ProMass to consider a target mass as “found”, the deconvoluted intensity must be above the Minimum Intensity setting.  If a target mass is found within the mass error tolerance limits but below this intensity, a red (not found) status will be reported.  The Minimum Intensity is set from the Reporting tab of the Build ZNova Params utility.
• Added capability of defining two regions of explicit spectral background subtraction, based on retention time. The subtraction regions are set from the Reporting tab of the Build ZNova Params utility.  These subtraction regions supersede any subtraction regions defined in the Xcalibur processing method.