Mascot Distiller Support

The current release of Mascot Distiller is version 2.3.2

If you are using an earlier version, you should install this free update. The functionality contained in optional toolboxes will only be enabled if included in your licence. Please contact sales@matrixscience.com for information about licence upgrades.

If you wish to evaluate Mascot Distiller, send an email request to support@matrixscience.com for a product key that can be registered on-line to obtain a 30 day licence. If you choose not to register, or after the 30 day period expires, Distiller will run in viewer mode, allowing you to browse existing projects but not modify them or create new ones.

Download Procedure

• Click on the following link and choose either to "Run this program from its current location" or "Save this program to disk". If you save the file to disk, then open it to execute the program.
• setup.exe (22 MB)
• The installer wizard will guide you through the installation / upgrade process. Extracts from the help file covering system requirements and installation are here
• Japanese language guide to installing or upgrading Mascot Distiller, (requires Adobe Acrobat).

System Requirements

The current release no longer supports Windows NT4. Mascot Distiller 2.1.1 will install on NT 4.0 SP6a, but the following file formats cannot be opened: Applied Biosystems Analyst, Applied Biosystems Data Explorer, Waters MassLynx, and mzXML. If you wish to work with these formats on NT4, you will need to install Mascot Distiller 2.0.0.

Documentation

Mascot Server Updates

Mascot Server 2.2

If you plan to use the Quantitation Toolbox, you can download an updated copy of quantitation.xml for your Mascot Server. (Right click the link and choose Save As.) This file is similar to the one in use on this site, and has more methods than the original file, and some settings for earlier methods have been updated.

Mascot Server 2.0

Updates can be downloaded using the following links. The Perl scripts should be copied to the Mascot cgi directory, while ms-searchcontrol.exe goes into the Mascot bin directory. For Unix, the files need to be un-tarred and you may need to change ownership and permissions to make the files executable by CGI processes.

• Mascot Server 2.0 for Windows
• Mascot Server 2.0 for Linux i86
• Mascot Server 2.0 for Tru64 on Alpha

Change History

2.3.2 (24-Dec-2009)

• 865: Added Mascot security password and username to command-line parameters
• 871: Need more flexible way to multi-select Bruker XMASS files for multi-file project
• 889: Std Err Threshold broken if simple ratio checked
• 890: Cannot Save As when project created by Daemon
• 897: Display more detailed error information when unable to load config files
• 900: Distiller crash during quantitation/li>
• 902: Crash caused by switching TIC units after peak picking
• 903: N-term modifications in quant table prefixed by '(c-term)'
• 905: Cannot select individual Masshunter files from multifile project dialog
• 906: Quant occasionally hangs if allow elution shift checked
• 908: Problems accessing SSL Mascot Server
• 910: Minor bugs in outlier rejection (quantitation)
• 911: Mascot server version 2.3 check not behaving correctly
• 913: May fail to display sample info if known file extensions are hidden in Windows Explorer

2.3.1 (17-Aug-2009)

• 856: If you clear 'Enable logging' you still get log messages from Distiller
• 858: Project file with components based on ambiguous variable mods caused crash
• 859: fitexy information not being saved in XML export
• 860: Crash as soon as click on anything in custom ratio dialog for replicate
• 866: Crash during quantitation when actual peak widths found to be less than minimum specified in processing options
• 867: Precursor methods with many components give garbage results for components 4 and above
• 868: Quantitation report, average protocol, intensity value can overflow
• 869: Crash during quantitation for large replicate protocol project
• 870: Crash when importing results from Mascot 2.1 server
• 872: Analyst Wiff provider mis-reading file header, can lead to large mass errors.
• 873: 'Save As' filters in common dialog wrong for mzData
• 876: Additional XML style sheets for copy and paste to Excel
• 882: Cannot open single Waters Masslynx file from multi-file project browse dialog
• 883: DPP overlay incorrectly scaled when time alignment is on

2.3.0 (25-Jun-2009)

• 502: Allow Fixed and variable modifications with same specificity
• 710: Need prompt to create local server entry on first run
• 725: Save As to same file name actually results in incremental save
• 762: Problems with terminus mods not being saved for in silico peptide fragmentation
• 764: Analyst multi-sample file with separate .scan cannot be opened if sample 1 is missing
• 776: Distiller sometimes crashes at point of trying to display quant table
• 777: Need to be able to load search results independently of quant results
• 778: Default licence directory is now C:\ProgramData\Matrix Science\licdb for Vista, Server 2008, and later.
• 783: When precursor charge is found in the file, if the value exceeds the maximum peak charge set in the processing options, reject the file value and continue as though it wasn't there.
• 785: Calculate XIC for peptide: doesn't work in Multifile projects.
• 786: Calculate an XIC often leads to crash
• 788: Can't create a project from a font: stuck if fonts folder becomes the default folder
• 789: TIC units not honoured when Mascot search submitted
• 790, 812: Command line mode to support Daemon automation
• 791: Add support for Average and Replicate protocols
• 795: If light component is missing, overlay for next component slips into this position
• 800: Add view-only mode when no valid licence present
• 804: Quantitation XML file has limit of 64 characters on filename
• 806: mzXML provider doesn't handle mixed profile/centroided data correctly + support for precision="64"
• 807: Default preferences fails to save state of "Allow user parameter fields in MGF peak lists"
• 809: Allow multi-select in Multifile projects dialog
• 809: Multi-threading used for quantitation
• 809: Saving of proxy or http access passwords; no longer have to embed in URL
• 813: Should be able to process time range in a multi-file project
• 816: Assert failure could occur with some Xcalibur files where zoom scans are present but aren't connected with MS2 scans.
• 820: Corrections could fail for multi-element corrections with high level of under-enrichment
• 821: For some Bruker files, MS3 scans could be attached to the wrong MS2 scan.
• 824: Added support for opening Analyst 1.5 files.
• 826: Quant treats Protein N-term mod as Any N-term when calculating m/z values for unmatched components
• 828: Search form emulation to support Internet Explorer 8
• 832: Mascot search of all tags is enabled for de novo solutions but doesn't work
• 833: Cannot create multifile project with mzXML files
• 837: Normalise on specified peptides or proteins
• 838: Added "Process This Scan" to scan context menu
• 839: Improved signal processing so that only the absolute minimum range of spectrum data is processed.
• 846: Fixed "Different scan types assigned to same group" assert failure that may occur when loading a peak list archive.
• 850: Incorrect processing options returned after loading peak list archive.
• New: Limit quantitation to unique peptides
• New: Offer to display report in web browser if Mascot search is error tolerant
• New: Option to use zoom scans for isotope tag-based methods
• New: Support Mascot 2.3 features, e.g. search multiple databases

2.2.1 (1-Oct-2008)

• 769: Fixed memory leaks and took steps to reduce memory fragmentation
• 779: Failing to save type of protein scoring to project file when it has been changed from default
• 780: Occasional crashes when allow elution time shift is true
• 781: Failing to re-calculate quantitation table when some format options are changed, e.g. require bold red
• 793: Crash if encounter MS3 scan without precursor information in Xcalibur file
• 803: Crash if no peptide matches in the first protein hit can be used for quantitation
• Add overlay option for TICs in multi-file project
• Better display of centroided spectra
• Clearer display when Allow elution time shift is true
• Clearer messages if quantitation not possible for some reason
• Crash if outlier method was undefined in quantitation method
• Creating a multi-file project prompted for developer toolbox licence
• Misleading error message when Distiller not permitted as client by Mascot security
• Number of hits in protein tree was AUTO even when fixed number specified in search
• Quantitation sometimes processed matches with scores below homology threshold when this was the peptide threshold type
• Support Arg to Pro conversion

2.2.0 (9-Sep-2008)

First release of Quantitation Toolbox

• 387: Sometimes need separate peak settings for MS and MS/MS.
• 454: Need some way of merging MUDPIT runs.
• 497: Implement support for MS3 and greater in time domain processing.
• 500: Conventional peak detection for reporter ions.
• 501: Finish implementation of data source verification using hash value.
• 517: User interface to create eXtracted Ion Chromatograms (XICs).
• 519: Group mascot results by protein in Explorer.
• 527: Ensure that regrid conserves relative area.
• 528: TIC minutes should display mins:secs as well as decimal minutes.
• 548: Display Expect value for PMF.
• 588: Peak areas are using bin width as x unit; should be Da.
• 589: Y axis intensity values displayed are out by factor 10.
• 608: Minor GUI annoyances.
• 612: Start sequence tag (11+) is confusing.
• 615: Need to handle more than 9 variable modifications because of exclusive mods.
• 625: Updates to distiller_mascot_search_2.xsd schema.
• 626: Decision logic to locate precursor charge in parent scan not always consistent.
• 627: Move tree management to App level.
• 634: Kratos provider not using the non linear calibration functions added at v13.
• 649: Support Kratos 'Auto' experiments.
• 652: Add new option to client.pl to return compressed result file without ions data.
• 653: Add stmobjFileModeFlagBinary to stream objects.
• 655: .rov file type not associated with Distiller on VISTA by default.
• 656: .rov files not opening on VISTA when double clicked.
• 664: Add distiller version to mgf file.
• 668: SDK CHM enum mdroDataSourceFormat_e missing mdroDataSourceFormatAgilentQTof.
• 670: Distiller fails to select user name in search form.
• 676: Group identical peptides in protein tree.
• 678: Unsupported scan type error is returned from Analyst provider if scan is empty.
• 681: Need to be able to access original peak data for centroided raw files.
• 683: Unknown scan types can break parent-child connections in the acquisition tree.
• 685: Rover crashes when trying to add a peak manually.
• 688: Crash after changing preferences.
• 690: MDRO properties dialog not sizing correctly for Japan Windows Locale.
• 691: Changes to Processing Options for Conventional PP.
• 695: Signal to noise will be incorrect for sparse spectrum.
• 696: S/N values need a little tweaking...
• 697: Misc. peak detection improvements.
• 699: Memoryleak in Voyager provider.
• 700: Add a property to return summed fit data within range of peaks only.
• 705: mzData export does not observe MaxPrecision setting.
• 712: Narrow m/z range baseline subtraction.
• 713: Need Minimum charge for MS processing in MDRO API.
• 714: Uncentroid peak width in properties dialog is out by factor of 2.35.
• 715: Peak list format options should allow user to choose area or S/N.
• 716: Crash when trying to submit search.
• 717: Zoom scans from Analyst and Xcalibur providers sometimes have precursor m/z and charge values.
• 718: Unable to use cached unimod.xml because of Invalid character error.
• 721: Add version to Distiller user agent string.
• 722: Accessing schema files on public server instead of local directory.
• 724: Unable to locate data source after saving project previously stored on another drive.
• 728: Add /LARGEADDRESSAWARE linker option to MascotDistiller.exe.
• 735: _DISTILLER_MDRO_VERSION and _DISTILLER_RAWFILE must be off by default.
• 736: Update XCalibur, MassLynx and Agilent libraries for Distiller 2.2.
• 737: Need to be able to specify charge state in API call when performing conventional peak picking (SPP).
• 738: Add licence feature for quantitation toolbox.
• 744: Add support for Launchpad 2.8 files.
• 747: Support formats that store both profile and centroided data.
• 751: Add support for Kratos spliced least squares calibration format files (QIT).
• 753: Bruker BAF shown as available when it's not.

2.1.1 (28-May-2007)

• 605, 644: Voyager provider now has native support for t2d files.
• 618: Compiled against new MassLynx API that fixes 2GB issue (no API changes).
• 633: Mass values in LMZ mode Kratos files were incorrect.
• 635: Fixed Bruker BAF file support for UltraFlex instruments and TOF-TOF files are now handled correctly.
• 643, 650, 654: New Agilent MassHunter (Q-TOF) provider
• 645: mzXML provider can handle files bigger than 2GB.
• 648: Xcalibur provider uses new Thermo XDK API.
• 638: Need to be able to specify proxy username and password.
• 631: Interface to web browser was failing with MSIE 7.
• 658: Add support for z+2 ions.
• 630: Lockspray should not be part of search toolbox.

2.1.0 (17-Aug-2006)

Mascot 2.2 If you try to connect to a Mascot 2.2 server using Mascot Distiller 2.1.0, the following error message will be displayed: This is because a new ions series has been added, (z+2H), that Distiller does not recognise. The fix is to update to Distiller 2.1.1. If you prefer to stay with version 2.1.0, download an updated copy of msparserU.dll and save it to the Mascot Distiller application directory, replacing the existing file.

• 223, 555, 559-562, 571, 579, 580, 597, 599: Bruker CDAL library adds support for BAF and XMASS ICR format files.
• 423, 547, 550, 552-556, 566, 567, 569, 570, 600: New Analyst provider removes dependency on the Analyst being installed.
• 465, 524, 580, 598: New Agilent TOF provider.
• 504: Failed to try guest login when Mascot security enabled
• 505: Added mzData as an additional peak list export format.
• 510: Was no prompt to save project when choosing Close All.
• 518, 521: Increased charge state limit from 8 to 40.
• 522, 551: Initial support for MassLynx lockspray scans.
• 526: Support negative charge states in Distiller UI
• 531: Blast link needs search both forward and reverse sequence
• 534: Fixed assertion failure caused when loading peak list archive that contained user-defined peaks.
• 538: Bruker trap file that doesn't end in ".d" causes error message "Catastrophic Failure"
• 539: Ignore negative mass values in mzXML files caused by CompassXport.
• 541: Implemented more regridding improvements to avoid assert failures. Discard any negative mass values at the start of a spectrum.
• 545: Protein names were not URL escaped when viewed in Distiller
• 549: Fixed issue that was causing Axima CFR calibration to be incorrect when data collection was set to automatic measurement mode.
• 563: Improved handling of Kratos files with multiple plate records but only one spectrum.
• 577, 581, 601: Added support for Kratos Axima 2.7 and LC-MS/MS files.
• 596: Fixed problems with loading a project file containing Mascot search results when original Mascot server was unavailable
• 610: If a long denovo was cancelled, would fail when tried again
• 611: Fixed invalid sequence tag queries created when charge state higher than 8
• 619: Fixed problem with Micorsoft IntelliType Pro Keyboard driver.

2.0.0 (29-Nov-2005)

• Display Mascot Search results within Mascot Distiller
• Automatic de novo sequencing
• Automatic sequence tag calling
• Manual de novo and sequence tag
• Predict fragment ions from a peptide sequence and overlay them on an MS/MS spectrum
• Predict mass values from a protein digest and overlay them on a spectrum

Other fixes and new functionality:

• 301, 377: Can output peak lists with de-charged precursors
• 354: Selecting project root node doesn't switch Processing Options
• 366: Export ASCII profile data
• 374: Peak list title can include unique peak list number
• 386: Check for update buttons were reversed
• 388: Number of decimal places used for precursor m/z in Dataset explorer needs to follow the setting in preferences.
• 395, 438: Improved performance when merging scans and reduced potential for "Unable to fit spectrum data" error after merge.
• 398, 426, 486: Modified scan aggregation logic so that it can handle a wider range of scan types better. Also, allow MS3 or greater to be processed when not doing time domain.
• 399, 486: Identify and process scans that have negative ion polarity correctly.
• 400: Added UTF-8 support.
• 401: Improved handling of file names with characters from non-Latin locales.
• 406, 421: Various performance tweaks and memory footprint reductions. LCMS-Solution: The "Last modified" header field value was incorrect. Analyst: Now returns the correct scan intensity values. Xcalibur: Added support for SIM and SRM scans.
• 408: Improved accuracy of regridding.
• 411: Reduced time taken when peak detection is required on survey scans during scan aggregation
• 420: Decimal places on the general tab should go up to 6. When profile data is exported, this is stuck on 3 dp
• 424: Output precursor intensity in peak list
• 434: Analyst: Reduced excessive logging which could sometimes occur when opening wiff files with the wrong version of Analyst installed.
• 445: MassLynx: Use Waters RAW API for accessing data files. Lock spray and reference scans are now identified as calibration scans. Implement temperature correction to Masslynx mass calibration (Thanks to Frank Morales of McGill University for assistance with this).
• 451: Crash if try to save multiple collection of multiple PMF peak lists
• 452, 476: Implemented MDRO project functionality
• 453: Cannot open MassLynx files with with certain service packs of Masslynx 4.0
• 460: Analyst: Modified scan numbering to account for empty scans.
• 466, 489: When there is more than one default precursor charge state assigned to a scan group, create a single peak list with multiple charge states instead of multiple linked peak lists.
• 467: "SCANS" and "RTINSECONDS" parameters can be added to MGF output.
• 468: Improved avoidance of division by zero during peak detection when noise spikes occur at the very end of a spectrum.
• 469, 488: Added support for mzXML input format.
• 479: Peak list table sometimes fails to display all rows
• 480: Xcalibur: Files that contained ECD scans were missing precursor m/z values.
• 481: Detect when baseline correction leaves no variation in the spectrum.
• 491: Allow control over the style of TIC to create.

1.1.2 (16-Dec-2004)

• 390: Axima CFR - values above precursor were incorrect for psd
• 394: Could not process QTrap file containing neutral loss scan
• 395, 438: Fix error when processing Analyst wiff file that reported "Unable to fit spectrum data - scan is probably corrupt"
• 404, 405: Add support for Shimadzu LCMSSolution LCMS-IT-TOF
• 413: Ignore non-MS functions in Masslynx, e.g. UV trace
• 415: Could not open Analyst Wiff file that contained just a single MS/MS scan, no survey or TIC
• 416: Access to Analyst Wiff files on remote drives requires call to CoInitialiseSecurity
• 418: Fix problem with Esquire data - aggregation of LC-MS/MS failed if first scan was MS2 followed by MS1
• 419: Fix error when processing Analyst wiff file that reported "The experiment type is not supported for processing"
• 422: Analyst file header: data type for DilutFactor different in QS and 1.3
• 427: Add support for Analyst QS 1.1
• 435: Change Axima QIT Options
• 437: Fix problems that broke interface to MassLynx 4.0 SP3 and higher

1.1.1 (7-Jun-2004)

• 364: Will attempt to obtain precursor information from *.t2d files when Voyager 4.3 or later is present
• 365: Fixed mass scale issues for next generation of QSTAR instruments - requires Analyst SP8 or later
• 372: If there was significant intensity at the very end of scan this could result in "#IND" values in the peak list
• 381: Added support for "SIM" type zoom scans in Xcalibur files
• 385: When parsing a text file, if unexpected data is encountered and no preceding valid data was found, then treat this as an error

1.1.0 (13-Dec-2003)

• 239: Fix localisation problems in Mass Deltas tab of Preferences dialog
• 241: Fix localisation problems in View; Range dialog
• 245: New View menu item to lock displayed mass range when moving between scans
• 246: Fixed problems with opening file in BioTools and Distiller at the same time
• 268: The last line of a text data file could be ignored. If the data were centroided, they might all be ignored if there were less than five peaks.
• 270: Made text file parsing more robust, particularly where extra values appear on the end of a line.
• 280: Fix problem with time axis when TIC zoomed in to very narrow range
• 281: Saving files in DTA format now saves a separate file for each spectrum
• 283: Peak list window could be hidden when changing main window size (Z order problem)
• 284: Crash when multiple rows of peak list window copied to clipboard
• 289: Update help to cover Masslynx 4.0
• 293: More frequent screen refreshes when saving large peak lists
• 295, 296: Fix problem opening Xcalibur files that have missing scan type in scan filter
• 297: Save peak list sub menu was taking a long time to display for very large peak lists
• 299: Deleted peaks were still output when a peak list was saved
• 300: Dataset Info Window was describing Masslynx files as Xcalibur
• 304: Fixed problem with Analyst QS file produced from a QSTAR XL instrument ("calib_t0 < 0")
• 307: Put check in code that apartment threading option is set correctly for Analyst QS
• 308, 327, 342, 353: Add support for Kratos Axima
• 311, 338, 339: Add code to check for updates on www.matrixscience.com automatically
• 319: Could get message "Tolerance range exceeded" if if the difference between the precursor m/z of two scans was exactly the same as the precursor tolerance value.
• 332: Introduced piece-wise calculation of S/N ratio because of spectra with very intense noise bursts in one place, (e.g. when laser fires)
• 337: Allow spectra to have non-monotonic mass scales (due to extrapolated polynomial calibration)
• 345: Fixed bugs in Dataset Explorer actions to expand all and collapse all
• 346: Better handling of corrupt Masslynx scans
• 349: Processing Options dialog did not display correctly with Japanese character set
• 352: Some drop down boxes in the processing options sheets allowed editing.
• 358: Xcalibur 1.4 FTMS data should be treated as compressed non-linear
• 359, 360: Interim support for *.t2d files from Applied Biosystems 4700 (TOF/TOF)

1.0.2 (24-Sep-2003)

• 273: Get garbage characters in licence request string if system has no NIC
• 278: Calibration constant ML3 in Bruker XMASS files was sometimes ignored
• 279: Mr values were being reported incorrectly because of an error in the mass of an electron; n.b. did not affect m/z values
• 290: Out of memory "bad allocation" error when processing large number of scans

1.0.1 (12-Aug-2003)

• 247: Tooltips for mass differences not displaying correctly
• 250: Crash on copying spectrum graphic to clipboard on NT4
• 251: Suppress error message if encounter empty scan in Xcalibur file
• 252: No link to context sensitive help for Mascot Server tab of preferences dialog
• 256: "Not a valid number" error message disables apply button in options dialog
• 257: DTA format should be disabled for MS data
• 260: Mini dump Message box is not application modal
• 261: Upper limit on m/z increased from 100,000 to 1,000,000
• 262: Peak processing errors produce generic error message rather than specific details
• 263: Duplicate mass values, especially in text data, caused by insufficient significant figures, should not be a fatal error
• 265: In the acquisition window, the project icon should have collapse all / expand all items on the context menu
• 272: On-line help glossary may be missing on some systems because of DLL missing from installation

1.0.0 (30-Jun-2003)

• First release