ProMass release notes
Changes in the current release, ProMass v. 2.8.5, ZNova v. 3.0.2
- 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
- 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
- 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.,:
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
- 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.