Mascot Parser Support

• Windows (Intel/AMD): 2.3.01
• Linux (Intel/AMD): 2.3.01
• Solaris (UltraSparc): 2.2.06
• AIX (P4/5): 2.2.01

To obtain Mascot Parser, read the licence agreement carefully, then enter your email address to obtain the download links.

If you just want to browse the help file, this can be downloaded as a Windows help file (chm). Some Windows security patches interfere with downloaded help files. If you cannot view topics, right-click the file, choose Properties, then Unblock. See this Microsoft KB article for further details.

System Requirements

Using the toolkit from Perl

Using the toolkit from Java

Using the toolkit from C++

Platform	Compilers supported
Microsoft Windows	Microsoft Visual C++ version 6.0 or later Microsoft Visual Studio .net 2003 Microsoft Visual Studio 2005 SP1 (32 bit and 64 bit) Microsoft Visual Studio 2008 SP1 (32 bit and 64 bit) Minimal GNU for Windows (MinGW) using g++ version 3.4.5 (mingw special) The library is supplied as a static .lib and as a DLL. In theory, it could be used with any compiler but since the implementation is C++ classes, it is probably only practical to use a Microsoft compiler due to disparate name mangling conventions.
Linux (x86 or x64)	Intel Linux compiler 11.1 or later, gnu g++ 3.4.6 or later. 32 bit and 64 bit shared and static libraries are provided.
IBM AIX	Visual Age C++ compiler 6.0 or later
Sun Solaris	Sun WorkShop 6, C++ 5.3 compiler

Change History

2.3.1 (29-Mar-2010)

• 17: Collapse peptides that, for example only differ with Isoleucine <-> Leucine with the new protein grouping.
• 117: ms_mascotresults::getNextSubsetProtein is now significantly faster.
• 511: Increase maximum number of enzyme cutters from 5 to 20.
• 523: Mascot security now works properly when specifying user_type=computer_name on Apache. (Had to use an IP address previously).
• 531: Allowed p value for significance threshold has been changed from 0 < p < 0.1 to 1E-18 < p < 1.
• 569: Change homology threshold reporting. Can now report a homology threshold value where the qmatch value is less than 100 and the version is Mascot 2.3 or later.
• 575: Session timeout now gives an error if the session file has been deleted and guest is enabled.
• 582: Support 64 bit Java for Windows.
• 583: Improved support for AMD processors in the ms_processors class.
• 584: Added a flag to ms_umod_configfile::save_buffer() to indicate whether to validate against the schema.
• 585: Added ms_tinycdb for giving access to tinycdb files.
• 587: Improve reliability of ms_mascotresults::isNA() for cases where there are no significant matches.
• 588: Add a function to return a 'histogram' for all ions scores.
• 589: Fix issue in ms_aahelper::calcFragmentsEx() which used to not take fixed modifications into account for searches where a quantitation method was specified.
• 590: Additional functions for multi-database searching in Mascot 2.3
• 593: Added function: ms_protein::getNumUniquePeptides().
• 594: Added function: ms_umod_modification::getRecordID().
• 595: Added functions to find accessions, descriptions, masses, sequences in summary reports.
• 598: Added support for Percolator.
• 600: Added function to retrieve flags and other parameters required for creating an ms_peptidesummary or ms_proteinsummary.
• 601: Quantitation: Support Multiplex with multiple ions series (e.g. for IPTL).
• 607: Call to delete should be delete [] in ms_mascotresfile destructor. Problem reported by valgrind, but no known issue reported.
• 613: Added a new flag to create an ms_peptidesummary object with no proteins. Useful for some reports.
• 615: Support for EMBL EST Taxonomy and Unigene. New enumeration: matrix_science::TAX_SPECIES_ACC2TAXID.

2.3.0 (17-Jun-2009)

198: Added matrix_science::ms_protein::getPepNumber() function, for when you're working bottom to top.
• 456: Added matrix_science::ms_mascotresfile::getMasses() function to create an ms_masses object from ms_mascotresfile.
• 465: Additional function for PMF iteration: matrix_science::ms_protein::getMasses.
• 471: Added the function matrix_science::ms_peptidesummary::getQueryList(QL_FLAG flag) for an easier repeat search. Requires Mascot 2.3
• 474: In security, add parameter to restrict spoofing. Additional security task: matrix_science::ms_security_tasks::SECTASK_SPOOFNAMEDGROUPSONLY and function matrix_science::ms_session::getSpoofableUsers() that is used in Mascot 2.3 ms-status.exe for the Show=MS_USERS command.
• 497: ms_umod_element::setMonoMass and setAvgMass now checks input parameters correctly.
• 514: Added a new matrix_science::ms_aahelper::ms_aahelper constructor to create an object based on the masses and modifications in a results file. Makes it easier to produce the tables found, for example in the peptide view table.
• 536: Added a function: matrix_science::ms_peptidesummary::getAllProteinsWithThisPepMatch.
• 538: Added matrix_science::ms_mascotresfile::getFastaPath to retrieve the path to the fasta file(s) used in a search.
• 540: Support Perl 5.10.
• 545: Added support for searches against multiple databases (introduced in Mascot 2.3).
• 551: Added functions matrix_science::ms_umod_configfile::getMajorVersion() and matrix_science::ms_umod_configfile::getMinorVersion().
• 552: Added matrix_science::ms_mascotoptions::getMinEtagMassDelta and matrix_science::ms_mascotoptions::getMaxEtagMassDelta.
• 556: Memoryleak in ms_modfile fixed.
• 557: Added matrix_science::ms_mascotoptions::getMaxDatabases function.
• 558: Support for Quantitation version 2 schema.
• 559: Added support for caching Mascot results.
• 560: Add basic support for ontology files in the .obo format. See ms_obofile.
• 561: Added a function ms_mascotresults::getQmatch to retrieve the the qmatch value from the results file
• 565: For Java, throw an exception if out of memory.
• 573: Quantitation reporter protocol: need to be able to specify a mod as required.
• 574: Added ms_peptidesummary::isPeptideUnique for quantitation support.
• 577: Finer control over progress reports. Changes docuemented in ms_mascotresfile::outputKeepAlive.
• 578: Experimental support for Python. Windows only initially.

2.2.08 (8-Jan-2009)

581: Support for Dunnington and Intel i7 processors (Linux)

2.2.07 (8-Jan-2009)

562: Support for Dunnington and Intel i7 processors (Windows)
• 563: Support for Power5+ processors (AIX).

2.2.06 (5-Sep-2008)

• 546: The function matrix_science::ms_masses.copyFrom leaves a dangling pointer.
• 550: Added statistical algroithm for use by Distiller to the Mascot utilities and tools module.

2.2.05 (26-Jun-2008)

• 509: ms_mascotresults::createUnassignedList did not free some memory when the ms_mascot_results object was deleted.
• 539: Add support for UltraSPARC T1 and T2, and IV+ processors .
• 543: Corrupt text could be caused by unicode characters in reference fields in unimod.xml. Error returns from Windows functions are now handled properly.

2.2.04 (5-Mar-2008)

• 493: ms_proteinsummary is 'wrong' for NA searches where there are hits from different frames. Instead of reporting a separate protein hit for each frame, the results are merged into one hit.
• 519: Support Java 6. Previous releases would occasionally crash with Java 6 on Windows.
• 520: Add ms_peptide::getNum13C function.
• 522: The example code, create_mgf.pl misses last peak.
• 526: Performance improvements in calls to getHomologyThreshold().
• 532: Support mingw.

2.2.03 (22-Jun-2007)

• 507: Trailing tabs in database definition line caused problems for some 3rd party software.
• 508: ms_modification::setNeutralLoss could not be called from java or perl.

2.2.02 (18-Apr-2007)

• 502: Failed to retrieve a remote configuration file when a proxy server requires a username and password to be specified.
• 504: Failed to retrieve a remote configuration file when using an https Mascot server.

2.2.01 (26-Mar-2007)

• 482: Changes to matrix_science::ms_datfile::updateForInstaller for Windows installer.

2.2.00 (15-Mar-2007)

• 485: Change matrix_science::ms_databases::findDatabase to allow searching of inactive databases
• 473: The limit of 64 databases should only count active databases
• 481: Added a function for Mascot installers to perform all required changes to mascot.dat. See matrix_science::ms_datfile::updateForInstaller()
• 470: standalone="no" is now omitted in xml-documents
• 466: Add new function: matrix_science::ms_processors::getNumCores()
• 462: Bugs in plpa library for 64 bit Linux fixed.
• 460: Increase limit on number of parse rules from 64 to 256
• 449: Homology threshold now uses the significance threshold value
• 447: Mudpit score now decreases when the significance threshold is decreased
• 453: Added matrix_science::ms_mascotoptions::getMaxVarMods() and matrix_science::ms_mascotoptions::getMaxEtVarMods()
• 448: Issue with leading space in comments when modifying mascot.dat fixed
• 446: There are no longer and unicode versions of the Parser library for Windows. Applications that are compiled with unicode support should still be able to link against the non-unicode versions of Parser
• 442: Curl support has never worked on 64 bit AIX and possibly other platforms
• 441: Unigene support has never worked properly on 64 bit AIX release, (and possibly SGI/Sun/Tru64). The 64 bit Linux versions were not affected by this issue
• 439: ShowSubsets is now a double rather than a boolean. Add matrix_science::ms_mascotoptions::getShowSubsets and allow matrix_science::ms_mascotoptions::setShowSubsets to take a double as well as a boolean value
• 414: 64 Bit Windows in now supported using Visual Studio 2005, service pack 1. This is available as a separate package
• 438: Add matrix_science::ms_mascotresults::MSRES_MAXHITS_OVERRIDES_MINPROB. See matrix_science::ms_peptidesummary::ms_peptidesummary for details.
• 437: Add security task matrix_science::ms_security_tasks::SECTASK_SEESEARCHINANYGROUP for the right to view searches for all users in all groups belonged to. Shouldn't require any changes to any third party applications that call matrix_science::ms_session::canResultsFileBeViewed
• 436: File Handle Leak in matrix_science::ms_mascotresfile with a zero byte file
• 435: Spaces at the start of all configuration files are now stripped.
• 434: A database name that starts with End is treated as the end of the database section.
• 427: matrix_science::ms_enzyme::verifyEnzyme doesn't complain about numbers in restrict and and also allows lower case letters.
• 430: Added z+2 series
• 154: Sort order for peptide summary with single etag - now sorted by delta.
• 253: Integra session files now get deleted properly. They now use the default timeout period.
• 293: When logging in using the 'guest' username, guest session files, such as guest_12312312313 session no longer get created.
• 295: Show Sub-sets is now a fraction, not boolean. See Grouping proteins together
• 298: matrix_science::ms_aahelper::createPeptide documentation improved.
• 320: File larger than 2Gb can now be read on 32bit parser.
• 335: Calling matrix_science::ms_mascotresults::createUnassignedList for a protein summary when there is no protein summary no longer gives errors, but just creates an empty list.
• 337: Mascot Integra users can no longer log in through Mascot - they must login through Integra.
• 343: Taxonomy strings can now contains commas.
• 393: Threshold cut-offs have changed. Old behaviour was to suppress the homology threshold if there were less than 1000 sequences in the search. New behaviour is to supress the threshold if qmatch is less than 100. There is also now a minimum for identity threshold of 13.
• 409: Verify enzyme used to return false if Restrict was empty
• 420: matrix_science::ms_mascotresults::getIonsScoreCorrected was incorrect if ITOL units were mmu rather than Da
• 421: Added matrix_science::ms_mascotoptions::getMudpitSwitch() and matrix_science::ms_mascotoptions::getSelectSwitch()
• 415: Support for minInternalMass and maxInternalMass. See matrix_science::ms_fragmentationrules::getMinInternalMass() matrix_science::ms_searchparams::getMinInternalMass() and matrix_science::ms_inputquery::getMinInternalMass()
• 413: New security params - varmods, varmods ET, num accessions. See matrix_science::ms_security_tasks::SECTASK_MAXVARMODS matrix_science::ms_security_tasks::SECTASK_MAXETVARMODS matrix_science::ms_security_tasks::SECTASK_MAXETACCESSIONS
• 410: Add PSI_MS_Name ( ex_code_name) and maybe Approved. See matrix_science::ms_umod_modification::getExCodeName() and matrix_science::ms_umod_modification::isApproved
• 408: Remove limit of 1024 mods - make it unlimited
• 397: Speed up ms_inputquery
• 396: Output keep alives in matrix_science::ms_peptidesummary::createUnassignedList()
• 394: Example C++ projects have the wrong compiler options for debug DLL versions
• 385: Added matrix_science::ms_inputquery::getScanNumbers() and matrix_science::ms_inputquery::getRetentionTimes()
• 384: mascot.dat Options functions missing: SortUnassigned etc.
• 358: getTagStart, getTagEnd, getTagSeries stuck in infinite loop
• 313: File format change in unigene files now processed properly
• 402: Add validation precedures to fragrules and enzymes
• 395: Keep alives need to be flushed. On Linux, the keep alive html comments are kept in a buffer and not flushed. This means, assuming that the standard text and default time of 5 seconds is used, that it takes 20 minutes for something to appear.
• 386: Support for mulitple neutral losses. The function matrix_science::ms_searchparams::getVarModsNeutralLosses which returns an array of neutral losses has been added. matrix_science::ms_searchparams::getVarModsPepNeutralLoss and matrix_science::ms_searchparams::getVarModsReqPepNeutralLoss have also been added.
• 387: The functions: matrix_science::ms_searchparams::getFixedModsName matrix_science::ms_searchparams::getFixedModsDelta matrix_science::ms_searchparams::getFixedModsNeutralLoss matrix_science::ms_searchparams::getFixedModsResidues have been added.
• 329: Return the new parts of the results file required for quantitation
• 332: Support decoy search results
• 338: New option ResultsFileFormatVersion in mascot.dat
• 355: Need to escape text in ms_inputquery::getINSTRUMENT() and ms_inputquery::getIT_MODS()
• 356: Need to read enzyme and taxonomy sections of resfile
• 373: getSeriesName returns empty string for ion series 19,20
• 376: setDelta() for unimod modification disables mod delta
• 326: If an old ICAT search is repeated with Mascot 2.2 or later, then the ICAT=ON should be translated to QUANTITATION=ICAT. The name 'ICAT' is retrieved from the options section of mascot.dat using getICATQuantitationMethod()
• 327: If the require bold red flag is set, then the wrong protein number used to appear in the yellow popup. The protein accession string was correct.
• 330: Support MODS and INSTRUMENT at the query level. See getINSTRUMENT(), getRULES() and getIT_MODS(). Needed for instruments that, for example, can switch between ETD and CID.
• 329: Support more than 9 variable mods. See Increase in the number of variable modifications for details on the impact of this to existing clients using Mascot Parser.
• 333: Add 3 new search parameters: getQUANTITATION() , getPEP_ISOTOPE_ERROR() and getDECOY()
• 248: Support for new PMF iterations introduced in Mascot 2.2. See: matrix_science::ms_mascotresfile::isPmfQueryUsed()
• 297: A Java or Perl application calling matrix_science::ms_aahelper::calcFragments can now access the fragments array.

2.1.02 (18-Oct-2005)

• 263: If a search was run using 'MONOISOTOPIC' rather than 'Monoisotopic', then a repeat search using search_form.pl would submit the second search using average masses because it doesn't recognise MONOISOTOPIC. This has been fixed in this parser release.
• 270: The Tru64 release of parser 1.x sometimes gives a different sort order for the concise protein summary due to a bug in the Tru64 compiler. This problem has been fixed in this release by using a patched Tru64 compiler.
• 276: Advanced topic! MSRES_DUPE_REMOVE_A will always be set which causes incorrect filtering when modifying these advanced flags. This does not affect any standard reports.
• 280: getNextSubsetProtein() now always returns false unless MSRES_SHOW_SUBSETS is set. This makes coding for the client a little easier and more transparent.
• 281: In cases where the highest scoring protein has no bold red peptides, selecting REQUIRE_BOLD_RED used to return no hits. Obviously, it is very rare for the highest scoring protein to not have any rank 1 peptide hits.
• 282: Add SECTASK_BIOTOOLSBATCH in preparation for next Bruker Biotools release. Added this task to the PowerUsers group.
• 283: Some customers still have systems with the electron mass being incorrect from the Mascot 1.9 installation. 'Fudge' the code by returning the correct value (0.000549) if the value in the file is 0.00549. If, for some bizarre reason, you really want the electron mass to be 0.00549, then specify it as 0.005490 in the masses file.
• 285: The matrix_science::ms_processors class now supports dual core AMD Opteron and reports that process affinity is available on Linux 2.6 kernels. Additional functions are now available to determine the name of the processor manufacturer and a description of the hyperthreading/multi-core/SMT functionality on the processor.
• 286: matrix_science::ms_protein::getFrame used to return -1 for protein database if the search was PMF. It now returns 0 as specified in the documentation.
• 287 and 290: Using the require bold red flag, it was possible to get occasional matches to proteins without any bold red peptides.

2.1.01 (24-Jun-2005)

• 261: Java version of ms_aahelper fails. C++ and Perl worked OK.
• 262: Passing a directory name rather than a file name caused a crash.
• 266: ms_searchparams::getUSERID returns -1 for old searches - meaning that it is impossible to see old searches unless the view all searches token is set.
• 267: In rare circumstances, a single peptide match generates multiple protein hits. Only happens at the random matching level and if minPepLenInPepSummary is non-zero.
• 267: getErrTolModMasterNeutralLoss() returned an incorrect value.
• 272: Java Parser on Linux fails to run.
• 273: Performance improvement for results files with matches to a large number of ambiguous residues

2.1.0 (30-Apr-2005)

• 2: Read and parse the Mascot configuration files.
• 122: Ambiguous residues coped with transparently.
• 126: Documentation - ms_searchparams class reference had multiple references to MASS=
• 142: ms_protein::getFrame() is now a const function
• 143: Documentation - now specifies that oneInXProb has lower limit of 10
• 144: Documentation - now specifies that 0 is returned for auto in matrix_science::ms_searchparams::getREPORT()
• 145: Documentation - matrix_science::ms_peptide::getIonsIntensity() is now clearer
• 146: Documentation - matrix_science::ms_peptide::getNumIonsMatched() is now clearer
• 151: Provide functions to calculate peptide and fragment masses. See Mascot utilities and tools module
• 162: Example perl script for protein summary and peptide summary have incorrect tag calls.
• 164: C++ test harness: peptide_list.cpp only builds on Windows.
• 173: Performing a search in the Windows msparser help no longer gives the same 'Title' for all pages.
• 175: Documentation - Ions series are now correct in matrix_science::ms_searchparams::getRULES()
• 183: Peptides with and without ambigious residues are now split into two entries. When decides whether to check if one protein is a sub-set of another it now compares the substituted peptide strings instead of original.
• 186: Mascot User authentication and login. See Mascot security and authentication module
• 187: Re-organise the help into separate modules, and provide example code in the examples directory as well as the online help.
• 199: Huge results files loaded and parsed using less memory.
• 200: AutoSelectCharge is a new parameter in the options section of mascot.dat
• 206: Before loading whole results file, check it really is a Mascot result file.
• 218: Support for negative charge state.
• 221: In the help, remove the class and class hierachy menu in the tree. These are now grouped together under the separate modules.

1.2.2 (19-Jan-2004)

• 121: Support for tag and etag additions in Mascot 2.0 result files has been added.
• 125: The C++ documentation referred to msparser.h where it should have been 'msparser.hpp'.
• 127: DLLMain is no longer defined in the Windows static C++ libraries.
• 128: Added matrix_science::ms_mascotresfile::getUniqueTaskID() to support taskid's used by Mascot Daemon in Mascot 2.0.
• 129: Fixed a crash for a faulty results file with the incorrect number of queries.
• 130: Sort order for proteins with identical scores used to be incorrect with .NET 2003 compiler, and Linux Intel compiler. Code generated by all other compilers was working properly.
• 132: getAvePeptideIdentityThreshold used to be incorrect for a search that has queries with no matches. Also, added matrix_science::ms_mascotresults::getMaxPeptideIdentityThreshold() as a safer option to display above the histogram on the Mascot 2.0 reports.
• 134: Support non-threaded build of Perl on Linux. Perl supplied with RedHat Linux is normally built with threads support. The default build of Perl (and therefore the one supplied with most other Linux distributions) has thread support disabled.
• 135: If a query contains a tag or an etag, then the homology threshold is now suppressed.
• 137: New protein scoring for MudPIT type searches.
• 139: Version string format in msparser.pm changed for more reliable version checking with different versions of perl.
• 140: Add matrix_science::ms_mascotresults::getProteinExpectationValue() and matrix_science::ms_mascotresults::getPeptideExpectationValue().

1.2.0 (20-Oct-2003)

• 5: Proteins with identical scores are now sorted by accesion number. If the accessions contain numbers (e.g. gi numbers), then the sorting is by the actual number. Otherwise, it sorts lexicographically. See also issue #48 below.
• 15: A warning message is now provided for duplicate accessions. Duplicate accessions are normally an indication of a faulty database, or incorrect parse rules, and should be investigated by the Mascot Administrator.
• 16: A new function matrix_science::ms_mascotresults::isNA can be called to determine if the search was against a protein database or a nucleic acid database.
• 36: Peptide mass fingerprint mixture mode is now supported. See Peptide mass fingerprint mixtures
• 40 and 102: Version information can now be found using the standard perl and java interfaces. Further information can be found at: matrix_science::ms_mascotresfile::getMSParserVersion()
• 42: Added a function to find number of proteins in the results. see matrix_science::ms_mascotresults::getNumberOfHits()
• 43: Added two new functions: matrix_science::ms_mascotresfile::enumerateSectionKeys matrix_science::ms_searchparams::getAllUSERParams to get 'user' parameters.
• 48: For a full protein summary report, the sort order now has a one to one correspondence with the entries in the results file. See also issue #5 above, which affects concise summary and peptide summaries.
• 49: Added a new function matrix_science::ms_mascotresults::getProteinScoreForHistogram to return the top 50 scores.
• 50: Issue with symbol log10: referenced symbol not found on some Solaris systems has been resolved.
• 54: A number of minor problems with the unassigned list have been resolved
• 56: Added two new functions: matrix_science::ms_inputquery::getPepTol() matrix_science::ms_inputquery::getPepTolUnits()
• 57: Changed matrix_science::ms_peptidesummary::getProteinsWithThisPepMatch to have an extra default parameter that returns quotes around the accession strings. This is required to allow accessions with spaces.
• 58: Add matrix_science::ms_protein::getUnmatchedMasses to get the list of observed mass values that failed to get a match to a protein hit in a PMF (listed at end of each hit in a protein summary report).
• 59: For a peptide summary, the probability cutoff calculation was not the same as in the Mascot 1.9 results reports, which use the average peptide probability. This is always a very minor difference.
• 60: Calculation for protein score in peptide summary is now exactly the same as in the Mascot 1.9 results reports. This resulted in very rare minor differences.
• 61: Error handler changes. IsValid() no longer returns false if there are only warning messages. Messages are now classified by severity. The test harness shows new code to print out warnings if the file is valid. Messages no longer have the file name at the beginning.
• 62: Added new function: matrix_science::ms_searchparams::getElectronMass().
• 71: Changes to the output of matrix_science::ms_mascotresults::getReadableVarMods for error tolerant search results.
• 72: Calling getProteinMass used to fail for hit number 50.
• 74: Option to 'leak bytes' to keep browser connection alive when a report is taking a long time to produce. See: matrix_science::ms_mascotresfile::ms_mascotresfile and matrix_science::ms_mascotresfile::outputKeepAlive()
• 76: Added a method for getting a protein or peptide summary for single hit very quickly. A parameter 'singleHit' has been added to both matrix_science::ms_peptidesummary::ms_peptidesummary and matrix_science::ms_proteinsummary::ms_proteinsummary.
• 77: Any SQ always used to return false - even for a sequence query.
• 78: Added matrix_science::ms_protein::getRMSDeltas to return RMS error for a protein.
• 79: Proteins in a protein summary are now collapsed by query number rather than peptide string. See Grouping proteins together for further information. This should give compatible results with Mascot 1.9 reports.
• 81: Key names in the results files are now always matched case insensitively.
• 82: Sample code for repeating a search is now provided in Perl, Java and C++ in the relevant 'test_' directory. See also Automated repeating of searches
• 83: Trying to read a result files from Mascot versions earlier than 1.02.00 will now produce an error. These files are not supported.
• 84, 85: matrix_science::ms_mascotresfile::getRepeatSearchString used to fail to return the peptol() parameter in cases where an override peptide tolerance had been specified. It also returned seq() instead of comp() for a composition query.
• 86: Minor differences in the output for an error tolerant search have been fixed.
• 91: Changed matrix_science::ms_peptidesummary::getProteinsWithThisPepMatch() is now considerably faster
• 92: Added matrix_science::ms_inputquery::getPepTolString()
• 93: The parameter minPepLenInPepSummary now behaves in the same way as the Mascot 1.9 reports. In the previous version, peptides shorter than this were totally ignored. Now, they are just ignored for Grouping proteins together purposes.
• 103: OneInXprobRnd is now a double rather than an int - it was previously possible to overflow this value.
• 104: Added a new function: matrix_science::ms_mascotresults::getSequenceMass to calculate the relative mass of a sequence.
• 110: The function: matrix_science::ms_peptide::getPrettyRank has changed. The ordering of the numbers is now slightly different and is consistent with the original Mascot reports.
• 113, 116: A bug in: matrix_science::ms_protein::getCoverage that caused to large a value to be reported (particularly with error tolerant searches) has been fixed. The getCoverage function is not supported for Mixture mode and Unigene - and will return 0 for these results.

1.0.1 (5-Mar-2003)

• 1: Add unigene support
• 28: ms_mascotresfile::anyMSMS function always returns false for one query
• 29: getRepeatSearchString() has line feed at end
• 30: peptide->getMrExperimental() can return 0
• 31: MSRES_REQUIRE_BOLD_RED doesn't work
• 32: Add option in C++ test harness to load parameters from configuration file
• 35: Error messages ERR_UNKNOWN… all one out
• 38: Corrupt title strings returned by ms_inputquery::getStringTitle(true)

1.0.0 (28-Nov-2002)

• First release