Versions 2.8.0 and later

This page contains historical information only. Please follow the links in the main technical support page for an up to date change log split by major version.

2.7.1 (14-Mar-2018)

• 13079: 32-bit MDRO installer images contain 64-bit binaries

2.7.0 (22-Jan-2018)

• 9622: Distiller chooses wrong peak for no obvious reason
• 9691: Distiller chooses wrong peak for no obvious reason
• 9834: Distiller single peak picking needs more work
• 9866: Distiller chooses wrong peak for no obvious reason
• 11210: Eliminate requirement to re-grid data
• 12483: Improvements to peak finding loop relating to charge states.
• 12945: Display the XIC overlay for precursor with a minimum of 1000 ppd
• 12960: Warn user if they have Windows 7 (or vista) compatibility mode selected

2.6.3 (25-Jul-2017)

• 12776: Small replicate crashes at end of quant

2.6.2 (24-Nov-2016)

• 11820: Crash on metabolic quantitation with modifications that have an element other than H,C,N,O,S

2.6.1 (10-Aug-2016)

• 11537: Re-structure peak list tab of explorer tree to display search results for chimeric spectra more clearly
• 12454: Sequence tag / de novo preferences should include options for J, O, and U
• 12464: Missing option for ppm for ITOL in preferences
• 12470: Moving reporter ion peaks from MS2 to MS3 needs to handle multiple children
• 12471: Missing instrument output dissociation type from peak list options format tab combo – PSD
• 12472: Missing fragmentation methods in preferences/peak list format on clean installation.
• 12474: Using ‘Processing->Create Summed Spectrum’ crashes Distiller
• 12491: Search results missing from peak lists tab of explorer in multi-file project
• 12492: New multi-file project drop down list only shows old options files
• 12525: Quant: when min peptides set to 1, get protein ratio of 0.0 for proteins with multiple PSMs but 1 unique peptide

2.6.0 (18-May-2016)

• 9359: Problem with empty survey scans in wiff files
• 9543: Want MDRO to contain further ‘structured’ file information
• 9630: Output an INSTRUMENT= line in mgf for mixed ETD/CID
• 9661: Cannot process Waters MS^E data
• 9835: Summing CID and HCD isn’t good enough
• 10723: Precursor doesn’t seem to work when component mods are variable
• 10807: No reliable way to reject one hit wonders in quantitation. Change to min_num_peptides
• 10929: Need to save Mascot server configuration to sub-projects
• 10982: Opening a very large mzML file can take a very long time
• 11146: Select to use percolator scores in Format options, but don’t perform decoy. Get no results – should get warning?
• 11250: Use the AB SCIEX WiffReader Library
• 11418: Add support for Waters lockmass
• 11440: Collapsing of matches
• 11472: fitexy element missing from quant.xml
• 11482: Quantitation XML does not include protein hit database index
• 11491: Distiller batch mode can hang when system is under load
• 11493: Need report for replicate that outputs intensity for each component
• 11565: Distiller takes ages to shut down with large project.
• 11579: Heavy isotope distribution incorrect for 13C metabolic quantitation
• 11704: MDRO throws error when raw file path contains unicode characters
• 11710: Quantitation is enabled by mistake
• 11739: HTTP Username and Password not set in ms_connection_settings
• 11750: Failure to re-determine precursor m/z in process all for Waters Synapt
• 11766: XIC and scan windows missing on opening project
• 11781: Xcalibur raw file gives error on opening
• 11786: Tree (SftTree) does not work on Windows 8 or Windows 10. Just a square blob is displayed
• 11812: Waters MassLynx data containing many DAD scans clutters Distiller scan list with ‘unknown class’ types.
• 11815: The peak list format options used need to be saved in the mgf header
• 11927: Browser reports always use old script if no search toolbox
• 12097: Crash in quantitaion in remove_duplicate_hits function for a multi-file, memory efficient project
• 12159: Installer changes for the the AB SCIEX WiffReader Library
• 12192: Additional summing options to be added to Processing Options property pages
• 12245: Add new option to PeakListFormatOptions COM interface. TitleIncludePSICV.
• 12285: Add an option to use Vendor Peak Picking
• 12312: Vendor Peak Picking support in Sciex Analyst provider
• 12313: Support new MDRO Experiment type DIA in tree items and tooltips.
• 12314: Vendor peak picking support.
• 12315: Support for Waters MassLynx MS^E data provider.
• 12346: Quantitation report validation fails with Error parsing ‘-1.#IND00′ as double datatype
• 12377: Changing component order in format options replicate tab causes crash
• 12417: Error handling when unable to open some part of a project
• 12423: Speed up peak list XML loading.
• 12425: The mechanism of remembering what peak list item was selected needs to be changed as it is too slow.
• 12441: Fix MS-Blast URL
• 12459: Change Spectrum mz order check from a fatal exception to a logged warning.

2.5.1 (19-Dec-2013)

• 11647: Crash on choosing to quantitate if the first scan in the file is empty or invalid

2.5.0 (27-Nov-2013)

• 10909: Protein view link fails to support multiple databases
• 10957: Cannot quantitate file from Daemon when security enabled unless already logged in using IE
• 11007: Problems with replicate tab of format options dialog
• 11165: MGF issues in multi-file project
• 11200: Disable normalisation for average
• 11224: Artefacts in spectrum display algorithm
• 11229: Errors in URLs for external browser reports
• 11230: Collapsing of matches to peptides with same m/z
• 11289: Cannot open a rov file which has unimod.xml with a residue of mass zero
• 11296: Distiller fails to error when given centroided scans for quantitation
• 11366: Multiple mods at a single site code is getting confused when peptide has multiple labels
• 11383: Time alignment failing for no obvious reason
• 11457: Crash when right-clicking on search results
• 11465: Project with average quant crashes if you change reference protein
• 11501: Time alignment of XICs to be redone to use centroids rather than fitexy
• 11524: No XIC peak for light component
• 11532: Display ratios greater than 999,999 in scientific notation
• 11533: Crash after setting simple integration to true after precursor quantitation
• 11535: Remove ‘(trapezium)’ from XIC label if simple integration fails with simpsons
• 11541: Crash when trying to open search report
• 11542: Peak list format options – MGF user parameters not used consistently
• 11549: Crash following incorrect password during server login
• 11552: Expose option in UI to save abbreviated quantitation XML
• 11553: Results cache ignored when re-loading project
• 11570: Problems with replicate quantitation
• 11577: Problems quantitating when method includes local mod definitions
• 11580: Problem Creating Multifile Project

2.4.3.3 (22-Oct-2012)

• 11351: Independent multi-file project may fail to consolidate quantitation results from all files

2.4.3.2 (21-Sep-2012)

• 11303: Crash immediately after choosing ¹⁸O quantitation

2.4.3.1 (6-Aug-2012)

• 11265: Workaround Xcalibur profile spectra returned from MSFileReader that contain decreasing m/z values

2.4.3 (26-Jul-2012)

• 10851, 10951: In quantitation table, collapse matches to different arrangements of mods that don’t affect the peptide m/z
• 10887: Update Distiller installer to include MSFileReader 2.2
• 10904: Second and subsequent MS/MS scans orphaned in Xcalibur Q Exactive data
• 10908: Allow exclusive quantitation label and variable modifications to target same residue
• 10927: No quantitation overlay for additional charge state matches
• 10933: Assert Failure: res < 0 [c:\backedup\chrisa\cvshome\mdro_2_4\mdro\src\engine\signal.h:348]
• 10934: XICs make no sense for centroid raw data
• 10945, 10973: Quant XML only lists first search result URL in multi-file project
• 10955: Improve regridding for compressed profile data with all zero intensity values removed
• 10956: Axima provider needs updating for files created with LaunchPad 2.9
• 10967: State of enable control in calibration dialog not being saved or displayed
• 10972: Precursor m/z taken from Xcalibur Q Exactive file has only 2 decimal places
• 10977: Baseline in spec window vanishes at high zoom
• 10993: Open multi-file project and change quant range causes crash
• 11021: Change labelling in new multi-file project dialog
• 11028: "Conversion error: Invalid input" when opening Xcalibur RAW file with multiplexing
• 11033: Keyboard interface to XIC window is broken
• 11064: Read-only mode should support command line export of quantitation XML
• 11137: Multifile project with small number of T2D files crashes
• 11214: Always regrid a profile spectrum returned from the text provider
• 11219: Fixed crash in Analyst provider for certain types of empty scans
• 11247: Integration failing occasionally when calculating ratio for replicate
• 11259: table_matches.xslt displays wrong component name in report for replicate

2.4.2 (18-Oct-2011)

• 10939: Consistency error when re-open multi-file project if MS/MS peak picking tab was disabled

2.4.1 (6-Oct-2011)

• 10916: PMF searches fail because charge not set to 1+
• 10915: Incorrect use of bold in proteins tree for family grouping
• 10907: Connection problem after specifying incorrect proxy server
• 10896: Problem with a Windows Mascot Server where the data directory is on different drive from programs
• 10894: Spectrum window y axis scale tick mark labels sometimes wrong
• 10892: Crash when loading search form after security session time-out
• 10889: Installing Distiller 2.4 may downgrade MSFileReader from 2.2 to 2.1
• 10884: Drop change password button from Mascot security login dialog
• 10881: Typo in search header text label
• 10880: Change label for process independently check box to clarify functionality
• 10879: Replicate tab in format options needs scroll bar
• 10878: Cannot save MS peak lists from LC-MS/MS dataset
• 10865: Command line -quantout displays dialogs when processing multi-file project
• 10863: Crash during quantitation of mzML due to accessing outside scan range
• 10858: Bruker XMASS / XTOF multi-file-select is broken in 64-bit
• 10856: Unable to process mzML file containing some empty spectra
• 10850: IIS integrated authentication broken for multi-file project
• 10848: Cannot submit very large searches (> 2 GB)
• 10847: Poor synchronisation between selections in trees and windows
• 10846: Need to be more intelligent in setting threads
• 10845: Add context menu option to delete peak list collection
• 10842: Explorer tree graphics disappear when Distiller loses focus on Win 7
• 10841: Set default scan selection to centre of XIC when quant fails
• 10840: Logfile for -batch not always saved to correct location
• 10837: Drop full path info from chro and scan window title bars
• 10835: In proteins tree, duplicate Peptide match nodes should be collapsed by default
• 10833: Remove Processing Options control from new multifile dialog after first project added
• 10829: Display progress bar when opening non-independent projects
• 10828: False test for change in threshold value in format options
• 10826: Avoid displaying node on search tree for duplicate master search
• 10825: Disable Mascot tag search in multi-file project
• 10779: Overlay can be inaccurate when baseline subtract set true unless peak widths very narrow
• 10742: Sequence ladder not displayed correctly for mass values over 10 kDa
• 9914: Peptide fragment masses stop at 10k in matched fragments table
• 9876: Quantitation fails for precursor method with 6 or more components
• 9767: Distiller minidump on crash not working correctly (DBGHELP.DLL not found)

2.4.0 (12-Aug-2011)

• New feature: 64-bit version
• New feature: Peak picking and quantitation are now threaded for speed
• New feature: Install Thermo MSFileReader to support Xcalibur
• New feature: Install Bruker CompassXtract to support various Bruker formats including maXis
• New feature: MzML support
• New feature: Independent processing of multi-file projects to avoid memory problems with very large projects
• New feature: Automatically fall through to simple integration when fitexy fails
• New feature: Support Percolator re-scoring
• New feature: Support Protein Family grouping
• 10780: Change definition of isPeptideUnique to be unique per family member rather than per family
• 10769: Bug in Rosners outlier code
• 10745: ms_mascotresfile doesn’t return INVALID_RESFILE
• 10698: Use ‘fast’ level of compression by default in project streams
• 10690: Make providers out of process…
• 10685: Assertion error ‘Month underflow’ if raw file acquired in January
• 10684: CreateSpectrum (and related) speed improvement
• 10670: Inconsistent calculation of m/z values when uncentroiding a spectrum
• 10669: Peak detection performance improvements
• 10666: Use cache files to speed project loading
• 10639: Add zip64 support to zip storage library
• 10627: On Windows, NTFS, cache files get re-created when going to/from Summer Time (Daylight savings)
• 10536: IgnoreIonsScoreBelow is converted to a score and rounded to an integer internally
• 9917: IgnoreIonsScore is double
• 9915: Display SD in italics if distribution NN
• 9909: Distiller truncates rather than rounds neutral losses so MetOx comes out at 63
• 9908: Distiller crashes if unknown scan types in the tree
• 9906: Search result import from command line should be just that
• 9901: Add Count/Size information to streams when possible
• 9897: Support Percolator
• 9896: Display FDR and search parameters in Explorer tree
• 9895: Support Protein Family grouping
• 9892: Process and Search menu item
• 9889: Need to restart Distiller to get new Quantitation method
• 9888: XRawFile sometimes returns an incorrect number of precursors
• 9887: Hard to explain numbers for simple ratio
• 9886: ‘Y Scale Up’ in View menu is actually an error message string
• 9885: Modification Carbamidomethyl%20(C) is not in the current list of modifications
• 9884: After upgrading to Distiller 2.3, Wizard crashes when opening a data source
• 9883: Name and email not saved in search form
• 9882: No proteins tab for PMF
• 9881: Unable to retrieve scan information from the data source. (1)
• 9880: Minimise reprocessing when quantitation options are changed
• 9878: Clicking on a peptide in quantitation tab causes a crash
• 9874: Quantitation result XML includes leading whitespace for N & C terminal modifications
• 9872: Regridding in summed scans is not correct
• 9870: Std Err threshold should reject matches where fit fails with result 999
• 9869: Error loading quantitation results but nothing in log
• 9868: Unable to retrieve scan information from the data source (Invalid Retention Time)
• 9867: Cannot open project created in 2.3.1
• 9864: Display error tolerant search matches
• 9853: N-term modifications in quant table prefixed by (c-term)
• 9850: Distiller crashes when quantitating protein 74 in this ion trap file
• 9848: Need mzML provider
• 9843: Mysterious Quantitation is cancelled. Normalisation method is reset to ‘none’
• 9842: Need to support Waters XEVO-TQMS data
• 9841: Isotope separation for satellite peaks due to under-enrichment incorrect?
• 9827: Distiller Workstation is missing functions provided in free viewer
• 9825: Add command line argument to export a quantitation report
• 9813: command line could have option to export and save quant XML file
• 9805: Disable Denovo when Always Uncentroid = false (MS/MS)
• 9690: Export de novo solution as CSV
• 9670: Drop Agilent Analyst provider
• 9659: Explorer tree, Peak tab, PMF should show which are the calibration scans.
• 9653: Message that Mascot server is off-line when you choose search
• 9621: Wait flag for CreatePeakLists
• 9591: Improve performance of peak processing, esp. on multi-core CPUs
• 9465: Change Search priority from Distiller
• 9442: Processing huge Masslynx file, containing just MS data, feels on the edge
• 9309: Distiller GUI can hang when using log window

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
• 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)

• 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 Microsoft IntelliType Pro Keyboard driver.

2.0.0 (29-Nov-2005)

Search Toolbox:

• 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 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 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