Mascot Distiller Support

The current release of Mascot Distiller is version 2.1.1

If you are using an earlier version, you should install this free update. Note that the functionality contained in optional toolboxes, such as the Search Toolbox, 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.

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 (17 MB)
• The installer wizard will guide you through the installation / upgrade process.
• Japanese language guides to installing or upgrading Mascot Distiller, (require Adobe Acrobat).

System Requirements

The current release will run under Windows NT 4.0 SP6a, but the following file formats cannot be opened: Applied Biosystems Analyst, Applied Biosystems Data Explorer, Waters MassLynx, mzXML. If you wish to work with these formats on NT4, an earlier release of Mascot Distiller can be downloaded here: Mascot Distiller 2.0.0

Server Side Updates

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

Mascot Distiller can now create MS/MS Peak lists having more than one precursor charge state, (because the charge could not be determined unambiguously). This makes it possible to submit MGF files to Mascot with multiple charge states, so that the charge state that gives the best match can be reported and the others discarded. This functionality requires Mascot Server 2.1.2 or later.

Known Issues with the current release

• When Windows Installer 3.1 has been installed on a machine (possibly via Automatic Updates) you may see a "Files In Use" dialog when Mascot Daemon is present and you are either removing or upgrading Mascot Distiller, Mascot Wizard or the old MDRO SDK. The dialog may request applications to be closed that have no relation to the product being removed. Provided that the relevant applications are not open it is safe to click the "Ignore" button. Another option is to manually stop the Mascot Daemon service and then click "Retry". This issue appears to be within Windows Installer itself
• 294: Saving a very large peak list is unacceptably slow under NT4. Other platforms are OK.

Change History

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