Mascot Distiller version 2.8

Mascot Distiller 2.8 requires 64-bit Windows 7 or later. Windows 10 and Windows 11 are fully supported.

Any version of Distiller 2.x can be updated to version 2.8 free of charge:

Downloading and installing instructions

Known Issues

Scaling issues with application level Windows scaling

There is a known issue if Windows is set to scale the Mascot Distiller Workstation GUI using ‘application’ level scaling. The symptoms are that the text on the explorer trees is too large and the spectrum or chromatogram graphics are outside the boundaries of their enclosing windows. To solve this issue:

• Ensure that ‘High DPI scaling’ setting for MascotDistiller.exe is not set to ‘Application’
• If you are connecting to the workstation with Mascot Distiller installed via a remote desktop connection, ensure that scaling is not set in the display settings on the remote system. Scaling should only be set on the client PC
• If Mascot Distiller is running on a VMWare hosted virtual machine, ensure that the Display scaling ‘Automatically adjust user interface size in the virtual machine’ option is unchecked in the settings for the virtual machine in VMWare Tools

Batch automation using Mascot Daemon 2.4 and earlier

If you are using Mascot Distiller as a data import filter in Mascot Daemon 2.4 or earlier, you need to run the Daemon ‘service’ component on the desktop. Otherwise, it may run out of resources. Details of how to make this change are in the Daemon help under In depth; Mascot Daemon Service. Briefly:

• Exit Mascot Daemon
• Select the entry for the Mascot Daemon Service in the Windows services control panel, right-click, and choose Properties
• Stop the service and set the startup type to disabled
• When Mascot Daemon is next launched, it will be unable to start the service and will display an error message
• Choose ignore

Exporting ion mobility values in peak lists using Mascot Daemon batch automation

If you are using Mascot Distiller as a data import filter in Mascot Daemon and you need to export ion mobility values in the generated MGF file, you need to enable a setting using the following procedure:

• Log into Windows as a user with Administrator privileges
• Type ‘cmd’ into the Windows search bar
• Right click over ‘Command Prompt’ and click ‘Run as Administrator’
• Navigate to the directory containing MascotDistiller.exe (by default this will be C:\Program Files\Matrix Science\Mascot Distiller)
• Run the following command:

  • MascotDistiller.exe -batch -daemonMGFIonMobilityParam 1

Bruker CompassXtract

Clean installations of certain 64-bit editions of Windows may be missing a Windows library required by Bruker CompassXtract. The symptoms are that the Bruker provider is unavailable in Distiller and you get error messages about msvcr71.dll being missing when Mascot Daemon starts up. The fix is to download msvcr71.dll and copy it to C:\Program Files (x86)\Bruker Daltonik\CompassXtract

Occasionally, when updating CompassXtract, the installation fails with error number 1935. The fix is to run a Windows registry cleaner, such as the one from Auslogics.

On Windows Server, when the installer tries to enable the .NET framework 3.5 feature (required by CompassXtract), it can fail with the following error:
Windows Server roles and features cannot be automatically installed or uninstalled via the Windows Features Control Panel.

If you encounter this issue:

• Cancel installation
• Manually enable the .NET Framework 3.5 feature from the Add Roles and Features Wizard in Server Manager
• Resume the Mascot Distiller installer.

Mascot Distiller stops working after Windows 10 update

A cumulative Windows 10 update can break the Visual C++ 2012 redistributable package shipped with Mascot Distiller. If either Mascot Distiller or Mascot Daemon stop working after completing a Windows Update, please go to Apps & Features in Control Panel, scroll down to Microsoft Visual C++ 2012 Redistributable and check the version shown for the x86 and the x64 packages.

If either one is not 11.0.61030, please try the following:

1. Close Mascot Distiller and Mascot Daemon
2. Download and install both the x86 and x64 versions of VC++ 2012 Redistributable Update 4 from here
3. Restart Mascot Distiller

Processing Thermo Orbitrap Astral data fails

When trying to process raw datasets created on the Thermo Orbitrap Astral, processing may fail with the error message “Proxy-stub communication error”. We are investigating this issue.

Change log

2.8.5 (05-Oct-2023)

• 14161: Fragment peptide feature top line confusing
• 14200: Protein descriptions in ANOVA plus Clustering report table are wrong
• 14440: Using multiply charged masses when copying the tag to the clipboard
• 14482: Tooltip for replicate data includes details for any point with the target scanid
• 14502: Newly imported PMF search results won’t expand on the Peaklists tree
• 14503: PMF protein match not shown on scanview unless the summed scan is already selected
• 14505: Optimise peptide range check for replicate XICs
• 14507: Default ETAG setting isn’t being honoured by newly created manual sequence tags
• 14511: Hierarchical Clustering report fails with equal ratio values

2.8.4 (28-Jun-2023)

• 13708: Failure to read charge state from file from Thermo Orbitrap Exploris 480
• 14296: Can’t change MS/MS processing options with Sciex wiff vendor peak picking for MS/MS peaklists
• 14313: Distiller crashes after saving project during Close or Close All call
• 14332: Update Agilent MassHunter libraries to add support for the 6546 LC/QTOF
• 14336: Peptides file of the stats export for replicate has incorrect component peptide scores and selected heading is wrong
• 14346: Pride project PXD0011050 time alignment fails
• 14347: Incorrect e-value being shown for SL matches
• 14353: Use average charge when setting mz limits in unsupervised time alignment for MS^E data
• 14370: msquantlib isn’t calling setPercolatorFeatures
• 14376: Volcano report table has repeated proteins with different values
• 14387: Include Visual C++ 2013 runtimes in the installer
• 14404: Python reports aren’t calling calling setPercolatorFeatures
• 14406: Disable the target FDR control in the GUI if results are percolated
• 14408: Fatal error from msquantlib library: ‘Invalid protein number X specified to quantitate. The protein summary contains Y hits’
• 14410: Manually called sequence tags are not decharging to 1+
• 14412: Deleted tags not being skipped when submit all tags selected
• 14413: Unclear axis labels on quality report
• 14418: Searching a multifile project without the search toolbox fails after the first search has completed

2.8.3 (12-Oct-2022)

• 14151: Check to see if display changes require requantitation is over-sensitive
• 14200: Protein descriptions in ANOVA plus Clustering report table are wrong
• 14202: Unclustered Table Headers in Hierarchical Clustering Report
• 14205: Table Peptides Report has incorrect protein ratios
• 14220: Time alignment offset calculation incorrect in some cases
• 14228: Creating a new project when connected to Mascot 2.6 or earlier fails
• 14232: Crash if using normalisation to specified proteins

2.8.2 (28-May-2022)

• 11474: Initial scan selection for XIC
• 11993: Implement fractions in LFQ
• 13082: Assert Failure: S/N is NaN
• 13809: Replicate quantitation fails if a subsearch has no protein hits
• 13906: De novo N and C term mods are not shown on the ladder or in the CSV export
• 13918: Save multi-file peak list collection as MGF and get “Fatal error: Value cannot be null.”
• 13920: If not logged in to Mascot Security when creating a new project, fatal error “Object reference not set to an instance of an object”
• 13930: Add frequency plots to Quality Report
• 13931: Update non stats graphs to use same format as stats graphs
• 13932: Adjusting Std.Err threshold in Distiller does not affect Quality Report graphs
• 13934: Unhelpful error message if you try and run quantitation from command line without the STB & QTB licence
• 13935: Need progress information when making tags for Search all tags and move to background thread
• 13939: ANOVA report displays incorrect ratio values
• 13941: PurifierDataSourceHeader class doesn’t check alternative paths for raw files
• 13944: In quantitation_2, allow multiple file_index values per component, and add ‘fraction’ for each file_index
• 13946: Expose Log2 ratio cut-off in Volcano plot report
• 13947: Volcano plot report displays incorrect ratio values
• 13954: Add GUI to set fraction sample map information for LFQ
• 13955: Support Replicate fractions in the GUI
• 13973: Correlation and matched fraction improvements for replicate
• 13974: Replicate quant. Save the correlation and matched fraction from each subproject in the master project
• 13975: Add Fraction(C1) Correlation(C1), Fraction(Ref), Correlation(Ref) etc. columns to table-peptides-int report
• 13983: Incorrect modification can be set to sequence ladder
• 13986: Would be nice if the directory for loading .rov files in a multifile project was remembered
• 13992: Average quant reports failing
• 13993: For new results the URL for opening in browser is not updated when you change display settings
• 13997: Error when re-opening a multifile project created from existing project files
• 13998: Export table used in volcano plot, log2 vs -Log10(pVal) as a CSV/excel table
• 14008: Support Replicate fractions in the API
• 14009: Segfault when exiting Distiller
• 14013: Recently used file list missing last file
• 14023: ms_cache_file readStream, writeStream and deleteStream are not thread safe
• 14026: Selecting Enzyme “None” on the Sequence tag / De novo preferences causes de novo to fail
• 14030: Bucket areas are not merged for replicate LFQ
• 14036: Support separate bucketArea values for each component in Replicate in merged results
• 14060: Spurious message about peptide failing intensity threshold in GUI
• 14062: Intensity threshold is testing against the component display intensity and not the total intensity
• 14064: Update the Method Configuration – Replicate documentation
• 14067: Add details of installing .NET 3.5 on Windows Server 2022 to the tech support page and release notes
• 14075: Crash in 14N/15N quantitation of timsTOF data
• 14076: Failed to initialise ms_customquantitation: Failed to load quantitation peptide match 24549 from the cdb file.
• 14077: Too much memory used for multifile quantitation with a large number of raw files
• 14083: Further thread safety issues in ms_mascotresfile
• 14084: Add new settings key which controls max number of projects to set LFQ peaklists metadata
• 14098: Crash from Proteins Tree when closing multifile project with unassigned list expanded
• 14101: Stream Objects tlb file not installed with SDK installation
• 14108: Rejected: Outlier message duplicated in tooltip and spurious fraction threshold failed message

2.8.1.1 (19-Nov-2021)

• 13949: Failed to save project after requantification

2.8.1 (04-Oct-2021)

• 12005: Why can’t preferences be saved and loaded?
• 12499: Multi-file project: when you remove a file, crash on closing application
• 12871: Sign the installer
• 13748: Cancel during process and search doesn’t kill running searches
• 13768: For replicate, improve the StdErr calculation
• 13772: XIC detection is sometimes selecting the wrong region
• 13777: Add a new Intensity MS1 XIC quality threshold
• 13778: Support intensity XIC quality filter in Distiller
• 13780: Log window log is not refreshed correctly when it’s closed and then re-opened
• 13781: Time estimate doesn’t increase if total progress is ‘stuck’ and rolls over after 24 hours
• 13800: FlexVariableTable.xml and ICRVariableTable.xml are missing from the 64-bit MDRO installation
• 13801: Add XSLT transformation to command line
• 13802: High memory usage with table_matches report
• 13833: Peptide quant status not always updated if you change the quality settings, resave then re-open
• 13837: With a replicate dataset, just opening ‘All options’ can cause a complete requant
• 13838: Can’t create a new multifile project from existing rov files if the Mascot server isn’t available
• 13842: Can not search a sequence tag against Mascot Server 2.2.06
• 13846: Update VC++ 2012 redistributable packages in the installer
• 13854: Create a new multifile project from existing sub-projects, process and search, get Fatal error:
• 13862: Parsing peaklist id from search or query title can fail
• 13863: LFQ is slow because of very long XICs when it just keeps looking for a peak
• 13867: Multithreaded performance issue
• 13877: Setting peaklist metadata leaves MDRO handle open until parent process closed
• 13879: Distiller command line should default to treating ‘Data source signature verification failed’ as warning, not fatal
• 13884: Specify the quantitation_2 schema to be taken from the build tree
• 13889: Suppress msparser proxy error after the first time it’s encountered
• 13890: Make the MS^E lockspray mismatch warning dialog permanently dismissible
• 13892: The ParserCacheFolder registry setting is not being used
• 13897: Encoding error from Chinese system for unimod_xl needs work around
• 13899: Support updated meaning for elution time delta in Replicate quantitation in the GUI
• 13905: Changing just the modifications doesn’t update the applied de novo search settings
• 13922: Javascript Error when opening a PMF or a SEQ+DECOY search form if Mascot server is 2.8

2.8.0 (11-Apr-2021)

• 9728: Vista UAC/virtualisation issues need addressing
• 9785: Have saved profiles to specify ‘everything’
• 9871: Time alignment for replicate
• 9877: Clicking on [Ignore] in SPP peak list, Mascot Distiller crashes
• 10665: Accessions are not URL-encoded fully when linking to protein_view.pl
• 10776: Columns in quantitation table should be sortable by clicking on headers
• 10795: Unable to select some modifications for nterm K when using fragmentation tool
• 10839: Locale problem
• 10852: Independent multi-file project should support replicate
• 10853: Peak-process a scan range then try to “Process and Search” – nothing happens
• 10914: Only delete results and peaklists from independent multi-file project files when the user saves the project
• 10940: Copy spectrum graphic to clipboard broken
• 11043: Manage multi-file project dialog is enabled for a single file project
• 11048: Crash if try to call seq tag off temporary peak list
• 11053: Enable copying of the protein digest table to the clipboard to export to Excel
• 11337: Need command line interface for de novo
• 11349: Typo in denovo csv export
• 11512: Sig threshold in format options needs to work for PMF
• 11585: Quantitation XML for an independent multi-file project is incomplete
• 11623: Cache file collision
• 11624: Search submit date is being changed when a project is saved
• 11650: Quantitation information in sub-project .rov files are incomplete
• 11675: Add the reference database name to the average quantitation protocol
• 11689: Speed up de novo by making it multi-threaded
• 11702: Only first component ms/ms peptide match exported in XML for replicate quantitation
• 11769: Global retention time alignment algorithm for label-free quantitation
• 11775: Local XML schema files should be updated from the Mascot Server being used
• 11905: When grouping all peptides for quantitation, the last rank is not included
• 12082: Does Distiller not show family members > 9 in merged results?
• 12371: De novo unassigned on independent multifile project only acts on loaded dataset
• 12402: Changing fraction or correlation threshold causes average quant to be repeated
• 12485: Bug in drawing SPP overlay
• 12734: In peak list table, charge column is alphabetical sort
• 12738: Crash if multi-sample wiff with empty first sample used in label-free multifile
• 12763: Manual sequence tags plus quantitation crashes
• 12826: Crash when creating a quant report after adding a new ratio
• 12827: Max threads drop down in default preferences
• 12867: Change MDRO apartment state to NTA
• 12938: PSMs in search results associated with wrong peak lists
• 12964: Cannot set max threads
• 12983: TIC units not saved correctly
• 13030: Install MSFileReader 3.1.9.0 to fix scan hierarchy problem with Lumos data
• 13031: Add MDRO version to tool tip for search result if available
• 13110: Not all matches to a user digest are showing in the table
• 13212: Invalid quantitation cache file when carrying out non-independent multifile precursor quantitation
• 13218: Add a provider for the new Bruker TimsTOF instrument format
• 13239: Memory efficient multifile puts tempfile as the search filename
• 13285: De novo solutions randomly go missing
• 13311: Tags sometimes have the wrong mass(es)
• 13362: Memory efficient multifile PMF project crashes when trying to merge search results
• 13364: Distiller sometimes treats a Save as a Save As for memory efficient multifile projects
• 13373: Truncated merge mgf file from memory efficient multifile project
• 13385: Command line quantitation with unsupported protocol causes crash
• 13465: Distiller includes old .opt files in drop-down menu even if they’re not present
• 13497: Normalisation doesn’t use quant results from all_charge_states matches if accession or peptide sequence specified
• 13597: Check for updates frequency does not stick or is not displayed correctly
• 13625: Ensure cursor isn’t shown across all XIC traces for a memory efficient replicate dataset
• 13626: Add method to get the library version
• 13671: Capture precursor info required for new label free quantitation code