Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

3.0 (30-September-2024)

  • 11568 Remove references to Integra and Insight in Mascot Security. Mascot Insight is no longer available.
  • 12892 Zero value for Observed in unassigned list for query whose only match is a chimeric duplicate
  • 13106 Add new method ms_inputquery::getQueryNumber().
  • 13447 Add ms_inputquery::getPeakCharge() method
  • 13480 get_ms_mascotresults_params() defaults to old protein grouping for sequence tag searches
  • 13531 Reduce the time spent in caching search results
  • 13678 Support new .msr file format
  • 14068 Remove directory gnu/7.2.0 from Linux shipper image. The directory duplicated the contents of the gnu/lib directory.
  • 14109 MascotFileProcessingThreads set to -1 should automatically use all possible threads. The default value is 4.
  • 14111 Rename ms_mascotresfile to ms_mascotresfile_dat. Only the class name changes. The rest of the methods and class members are identical to Parser 2.8. Please see the migration instructions in Upgrading to Mascot Parser 3.0.x from 2.8.x.
  • 14121 New API for .msr results files, and implement parsing and interpretation of MSR v0.9 files. Mascot Search Results (MSR) is a new format in Mascot Server 3.0. MSR v0.9 was an intermediate format leading up to MSR v1.0.
  • 14127 Support for Visual Studio 2012 and 2013 has now been dropped. This change only affects the statically linked msparser.lib. If you are still using these compilers, please link dynamically against msparser.dll.
  • 14157 Undefined behaviour in ms_fdr_query_processor::getThresholdForFDR() when comparing pointer address to integer zero. Fixed due to a compiler warning. The fault made no observable difference to the algorithm.
  • 14179 MinGW instructions have been reviewed and tested using MinGW GCC 12.1.
  • 14192 C++ shippers on Linux are now compiled width GCC 5.5.0, and MinGW on Windows with GCC 7.1.0. If you are using the Parser static C++ library, please upgrade your compiler to GCC 5.5 or newer (Linux) or GCC 7.1 or newer (MinGW). If you are using the shared library, earlier compiler versions may be compatible.
  • 14208 ms_searchparams::getVarModsNeutralLosses() doesn’t return satellite NLs.
  • 14217 Failing to read query-level mods NL string, fault introduced in Parser 2.7.0.
  • 14240 New mascot.dat option SearchSubmitOutputFormat. The setting is used by the Mascot Server web-based search form (search_form.pl). The setting defaults to ‘msr’, which is the new file format in Mascot Server 3.0.
  • 14247 New mascot.dat option to diagnose MSR generation.
  • 14257 Move Quantlib/Distiller time alignment code to Parser and save/load in cdb/xml
  • 14262 TMTpro 16-plex and 18-plex mod groups should be required=false
  • 14274 Methods and classes not wrapped properly by SWIG for Perl, Python, Java and C#
  • 14285 Implement New Imputation Methods in Parser. ms_imputation is experimental in Parser 3.0 and may be changed in a future release.
  • 14293 Further thread safety issues : matrix_science::ms_mascotresults::getPeptideThreshold. This method is now safe to call from multiple threads.
  • 14315 Add getStage method to ms_http_client_search
  • 14320 Update Doxygen to version 1.9.6.
  • 14323 ms_ms1quantitation should allow a search without a quantitation method to load replicate or average results.
  • 14337 Roll-up of changes to API doc and release notes for 3.0
  • 14361 ms_inputquery::getPeakMass(): Ions2 and Ions3 lines are missing the first peak. Ions2 and Ions3 lines in .dat format contain data entered with the rarely used ions(b-…) and ions(y-…) qualifiers. ms_inputquery::getPeakMass() and getPeakIntensity() accidentally skipped the first mass in the list.
  • 14377 getQmatch() returns INT_MAX if called with non-existent query number, should return 0.
  • 14389 Implement schema changes for MSR v0.99; implement MSR parsing/processing for v0.99; fix bugs in MSR parsing/processing; implement schema changes for SDB v0.99; implement SDB writing/processing for v0.99; fix bugs in SDB parsing/processing; rename headers
  • 14392 Add MSR files to the Parser test harness
  • 14422 Support MSR file download in new method ms_http_client_search::downloadResultsFileMSR()
  • 14432 Add streaming decompression to ms_zip
  • 14433 Parser should give a warning if reading a file from future version of Mascot
  • 14441 New Parser class for retrieving MSR file in .dat format
  • 14445 New option AlwaysCreateDat28ResultsFile. The setting is used by the Mascot Server search engine (nph-mascot.exe). The setting defaults to 0 (false) – Mascot Server 3.0 and later default to writing search results in MSR format.
  • 14481 All methods of ms_inputquery should be const.
  • 14483 Documentation for ms_inputquery::getNumUsed() was incorrect. This method always returns 0.
  • 14544 Change ms_modfile private member std::auto_ptr to std::unique_ptr
  • 14549 Display emPAI in integrated error tolerant searches
  • 14551 ms_searchparams::getLIBRARY_SEARCH() returns -1 when LIBRARY_SEARCH=1 in search params
  • 14553 Remove ms_mascotoptions::getSeparateLockMem()
  • 14554 Compile SWIG modules with GCC11 and VS2019 (Perl, Python, C#, Java)
  • 14558 Update SWIG to 4.2.1
  • 14571 Unstable order of sameset accessions in integrated SL searches
  • 14577 Add wrapper for Perl 5.36 on Linux
  • 14578 Add new method ms_mascotresfilebase::getSLExecCommand()
  • 14588 Add accessor method ms_ms2quantitation::getPeptideSummary()
  • 14590 Update ms_ms1quantitation::mergeQuantitationResults() to support MSR
  • 14636 ms_fileutilities::getLastModificationTime() fails on Windows if the file has been opened without shared read access
  • 14637 Drop version-specific Python libraries and ship a single ‘universal’ library
  • 14647 New argument to ms_mascotresfilebase::setPercolatorFeatures(): a vector of ML adapter parameters. The argument is optional and defaults to empty vector.
  • 14649 ms_mascotresfilebase constructor, if XMLschemaDirectory is empty string, treat it the same as null pointer
  • 14665 Add a ms_modification::getClassification() method
  • 14673 ms_linker_site_vector fails to initialise alpha and beta peptide lengths to zero
  • 14674 Add quantitation option to choose type of time alignment
  • 14692 Internal shipper for Perl 5.38 built with VS2019 and GCC 11
  • 14707 ms_datfile::updateForInstaller(), replace ResultsCache with a default
  • 14748 New methods ms_searchparams::getPERCOLATE() and ms_searchparams::getML_ADAPTER_PARAM()
  • 14749 When setting Percolator flag in ms_mascotresfilebase::get_ms_mascotresults_params(), check the new search param PERCOLATE, then mascot.dat options
  • 14750 ms_mascotresfilebase::get_ms_mascotresults_params() treats DECOY=-1 as DECOY=1 when deciding whether to set MSPEPSUM_PERCOLATOR
  • 14752 ms_mascotresfilebase::get_ms_mascotresults_params() should not set MSPEPSUM_PERCOLATOR for error tolerant search
  • 14766 Update unimod.xml and unimod_xl.xml to the latest versions for 3.0
  • 14775 Python msparser library cannot be used with xgboost or tensorflow libraries
  • 14776 ms_datfile::updateForInstaller(), change SplitNumberOfQueries from 1000 to 2000
  • 14777 New option CreateLegacyModAndSubstitutionFiles
  • 14778 New option AlwaysEnableAutoDecoySearch
  • 14785 ms_datfile::updateForInstaller(), set PercolatorUseRT to 0
  • 14789 New mascot.dat option SearchSubmitAcceptedFileTypes
  • 14795 ms_ms1quant_time_align::getRToffset() looks in wrong part of array in some cases
  • 14797 LabelAll option is obsolete
  • 14811 Quantitation method for TMT 32/35-plex
  • 14820 Default to sequence FDR in ms_mascotresfilebase::get_ms_mascotresults_params()
  • 14821 ms_ms1quant_time_align::getRToffset() code is not treating the “to” consensus and “from” consensus properly
  • 14833 Change behavior of ms_mascotresfilebase::get_ms_mascotresults_params() to set the target FDR
  • 14844 Add new method ms_masses::saveToString()

2.8.1 (31-March-2022)

  • 13751 Add shippers for Python 3.7, 3.8, 3.9
  • 13766 502.2 – Bad Gateway on opening search results, caused by segfault while reading empty protein description
  • 13864 Sorting unassigned list fails if filtering is active, caused by findPeptides() always returning results in query order
  • 13927 Start and end of quantitation match range can be reversed causing out of memory
  • 13961 Error message 539 lacks information – relevant taxonomy node files now added to error message
  • 13962 Dodgy protein inference when two interlinked proteins have the same very short beta peptide
  • 13963 Add TMTpro 18plex quant method
  • 13989 Xml configuration files should not be written in place
  • 14000 Increase limit of taxonomy choice include/exclude line length – new limit is 32kB

2.8.0 (28-Jul-2021)

  • 12447 Calculate an expect value for error tolerant matches. See Error tolerant searches.
  • 13357 End of 32-bit Parser on Windows. Parser 2.8 and later are now 64-bit only on all platforms.
  • 13378 Section title “Using STL classes” should mention vectord, vectori, VectorString
  • 13406 getThresholdForFDRAboveIdentity() doesn’t always work when Percolator is enabled
  • 13514 Parser 2.7.0 C# is built with VS2015, not VS2012
  • 13604 New setting for number of input file parsing threads
  • 13633 updateForInstaller: replace PercolatorFeatures with new feature set
  • 13634 New options PercolatorTargetRankScoreThreshold and PercolatorTargetRankRelativeThreshold
  • 13639 Add static and shared libraries for VS2017. Parser 2.8 ships with libraries compiled for VS2012, VS2013, VS2015 and VS2017.
  • 13663 ms_aahelper never returns internal ions over 700 Da
  • 13673 ms_proteinsummary needs to check inference flags
  • 13696 New parameter for ms-createpip.exe multithreading
  • 13715 Only return false from getThresholdForFDRAboveHomology() if closest FDR is not within a factor of 2 of target FDR
  • 13716 Make ms_searchparams thread safe and more efficient
  • 13726 Logging and error handling documentation is mostly missing
  • 13730 Allow zero child elements in mxm:accessions, mxm:filters, mxm:scope, mxm:settings
  • 13746 Remove ICC2016 shippers. The GCC 4.8.5 static and shared libraries now shipped with Parser can be used with both GCC 4.8.5 and later, and Intel® Compiler 2016 and later. See C++ toolkit installation on Unix.
  • 13759 New ms_peptidesummary parameters: target FDR and FDR type. See Target-decoy searches and false discovery rate.
  • 13763 Add willCreateCache methods which take a ms_mascotresults_params argument
  • 13769 Update unimod.xml and unimod_xl.xml for 2.8.0
  • 13806 Target FDR algorithm: maximise the number of target matches if FDR is 0%
  • 13808 Update element descriptions in crosslinking schema for the crosslinking configuration editor
  • 13818 If alpha and beta are in different proteins, one of them is not assigned to any protein
  • 13848 Add Parser targets for Perl 5.32 and 5.34 (Linux) and Perl 5.32 (Windows).

2.7.1 (11-Apr-2021)

  • 11666 Add MS1 quantitation result reading to msparser
  • 12409 ms_ms1quantitation needs to handle normalisation
  • 13548 ms_http_client_session::submitSearch should be able to use -batch option
  • 13556 Schema changes required for Mascot Distiller 2.8
  • 13607 Multiple issues with ms_quant_helper::isPeptideQuantifiable for MS1 based quantitation
  • 13614 MS1 quantitation, XML output, Hit ratio set to invalid when it should be valid
  • 13667 ms_quant_helper VarModStringToVector doesn’t handle letters correctly
  • 13686 ms_xic is not thread safe
  • 13702 Memory leak in mshandle
  • 13725 HTTP authentication fails if POST request redirects to GET (e.g. search with -batch mode)
  • 13743 More problems with ms_quant_helper
  • 13760 Missing and additional protein ratios for Precursor quantitation when mass-time-match is enabled

2.7.0 (27-Jan-2020)

  • 10427 ms_aahelper needs argument to generate mass values for all neutral losses
  • 10714 Parser error handling is not thread safe
  • 10752 Satellite ions should not be restricted to fragments containing R
  • 10793 findPeptides() with FT_PEPTIDE_EXP_MZ and FC_SEARCH_ALL_RANKS returns all ranks with no match
  • 11802 Python example script emits “query out of range” errors and crashes
  • 12100 single underscore character identifier is defined in des.h
  • 12326 Add switch to mascot.dat to over-ride asynchronous search submission (batch mode)
  • 12493 Add an internal interface for fast conversions between strings and numbers
  • 12496 Disallow creating a database whose name differs from an existing one only by case
  • 12624 Use cache files from 2.4 and 2.5 in test harness to ensure backwards compatibility won’t break
  • 12672 ms_mascotoptions setters should check the limits or be removed
  • 12753 ms_tinycdb openIndexFile uses string comparison on gmt timestamps to check file dates
  • 12808 ms_umod_configfile::findModification should be optimised with a lookup table
  • 12820 Add a clear() method to ms_progress_info
  • 12832 Expand parser test harness with files combining, mod search and ambiguity groups
  • 12857 Potential crash when sorting peptides
  • 12860 willCreateCache adds errors to the ms_mascotresfile object, resulting in duplicates
  • 12863 Search modification by name with findPeptides returns only one value on Windows
  • 12888 Add a documentation page for the FDR procedure
  • 12891 Test harness scripts should be converted to python
  • 12895 Add a utility function to compare XML files
  • 12902 Modification statistics for error tolerant search can be highly misleading
  • 12913 Revert to just saving rank 1 in percolator pip file
  • 12921 Add PSM and sequences used for ID to proteinHit element of quant XML export
  • 12924 Peptide summary cache file name is different between master_results and ms-searchcontrol
  • 12932 Support for Visual Studio 2005, 2008 and 2010 has now been dropped.
  • 12959 Added XML export to ms_ms2quantitation and cdb file export and import to record user protein-peptide ratio selections. The following methods have been renamed and moved to ms_quantitation from ms_ms1quantitation: addHeaderInfo renamed to addHeaderField, addRawFileInfo renamed to addRawFileField, clearHeaderInfo renamed to clearHeaderFields and clearRawFileInfo renamed to clearRawFileFields.
  • 12936 Report of Error tolerant search does not display all matches when None is selected
  • 12937 Update from SWIG 2.0.12 to SWIG 3.0.12 for ALL languages supported by Parser
  • 12950 Compile Parser with GCC 4.8.5
  • 12951 Support for GCC 4.1 and Intel Parallel Studio XE 2013 has now been dropped. Static libraries on Linux are compiled with GCC 4.8.5 and Intel Parallel Studio XE 2016. Support for 32-bit Linux has been dropped.
  • 12977 Support for Perl 5.8 to Perl 5.14 has been dropped on Linux. Support for Perl 5.28 and 5.30 has been added on Linux.
  • Support for Perl 5.8 to Perl 5.16 has been dropped on Windows. Support for Perl 5.24, 5.26, 5.28 and 5.30 has been added on Windows.
  • 12990 Logging: Improvements for ms_loggingmonitor required including better documentation
  • 13020 I don’t believe PSM and PepSeq counts for Percolated results
  • 13029 Add ActivePerl 5.24, 5.26, 5.28, 5.30 build targets on Linux
  • 13033 .MSP File Format Issues (Was Error message text for ERR_MSP_NIST_MSP_NO_SPECTRA is misleading)
  • 13047 Crosslinking changes for protein inference and Parser results file API
  • 13048 Why are a third of the tests slower on Windows compared to Linux?
  • 13101 Add support for Python 3.6
  • 13108 .MSP File Format Issues #2
  • 13122 Mascot Server reporters error with ms-ms data when variable reporter ion modifications are selected
  • 13124 Segfault when caching an iTRAQ 4-plex file with variable mod group
  • 13200 New ms_peptidesummary constructor parameter: minimum number of significant unique sequences
  • 13203 Make ms_mascotresfile more const
  • 13230 ms_mascotresfile::appendResfile() generates lots of XML errors unless used on Mascot Server
  • 13234 Crosslinking method definition API and class structure
  • 13241 Description of getMaxPepModArrangements method in the documentation is confusing
  • 13243 Update unimod.xml to the latest one
  • 13268 ms_peptidesummary::isDataCached() returns false for BUGFIX_12740
  • 13276 ms_mascotresfile::getMasses() sets electron mass to 0.0 for results files from 1.9 and earlier
  • 13278 ms_aahelper must support ET and library mods
  • 13284 DEFAULT_MINPEPLENINPEPSUMMARY should be 7
  • 13288 ms_fragment needs a constructor for precursor NL peaks
  • 13294 Replace Numerical Recipes code with ALGLIB
  • 13301 Add flanking residues to the distiller xml MS1 quantitation results export
  • 13310 Peptide without required fixed mod for Reporter quant incorrectly has quant ratios
  • 13312 Add new option in ms_mascotoptions for suppressing PIP file creation during the search
  • 13315 Review default crosslinking methods in crosslinking.xml
  • 13324 New method ms_mascotresults::getDiscoveredLocalModDeltas(), and output order of getDiscoveredErrTolModDeltas() is ambiguous
  • 13409 ms_peptide::getIonsScore() and ms_mascoresults::getIonsScore() return different values with same args.
  • 13437 Add Options: DechargeFragmentPeaks

2.6.2 (14-Apr-2018)

  • 10731 ms_processors produces bogus results for more than 64 logical CPUs.
  • 12944 Last pretty rank 2 peptide incorrectly assigned to a protein in ms_peptidesummary cache file, caused by dangerous map deletion during iteration.
  • 13064 New option UseHTTPProxyForHTTPS available from ms_mascotoptions::isUseHTTPProxyForHTTPS and ms_connection_settings::isUseHTTPProxyForHTTPS.

2.6.1 (02-Jun-2017)

  • 12276 Documentation changes for schema paths with spaces. See, for example: ms_distiller_data::loadXmlFile.
  • 12538 Performance improvements when expanding proteins etc. in a 3GB results file. Used to take several minutes with some files.
  • 12606 The rank argument of ms_mascotresults::getHomologyThreshold has been changed from an int to an enum.
  • 12642 Add functionality to allow a specified range of spectra in an MSP file to be exported/saved. Additional parameters for ms_spectral_lib_file::saveAs.
  • 12643 Add Parameter in the options section of mascot.dat to specify max number of spectra in a block. See ms_mascotoptions::getSpectraPerLibraryBlock.
  • 12656 Segmentation fault if you pass null as filename to ms_mascotresfile has been fixed.
  • 12657 New parameter in options section: number of peaks per 100 Da to choose from observed spectrum when creating library spectrum. See ms_mascotoptions::getCrawlerNumPeaksPer100Da.
  • 12683 User entered sensitivity count or significance threshold not working as expected for low scores in library-only search.
  • 12689 Fixed small memory leaks in ms_datfile, ms_mascotoptions and ms_processors.
  • 12695 Supply additional schema files to support reading of Distiller xml files.
  • 12704 New functions, ms_mascotresfile::getSLFragmentTolerance and ms_mascotresfile::getSLFragmentToleranceUnit for reading spectral library fragment tolerance.
  • 12717 Minor peptide sorting changes for duplicate peptides from spectral libraries.
  • 12721 Calling the function willCreateCache used to create the directory if it didn’t exist.
  • 12724 Change default value for ms_mascotoptions::getPepSearchTool
  • 12729 When searching two or more spectral libraries mapped to the same reference, all the proteins reported are to the same SL in master_results_2
  • 12731 Added a new methods for annotating an MSP spectrum : ms_spectral_lib_entry::annotatePeaks and ms_spectral_lib_peak_list::annotatePeaks.
  • 12737 Fixed a segmentation fault if you call setReferenceFasta() before setToleranceInDa() or setToleranceInPPM()
  • 12740 With Percolator enabled get “Protein: KLH40_HUMAN has 1 cached, but 0 from the re-load”.
  • 12749 Added support for std::wstring in C#.

2.6.0 (13-Dec-2016)

  • 11481 Improvements to ms_peptidesummary::getThresholdForFDRAboveHomology and ms_peptidesummary::getThresholdForFDRAboveIdentity.
  • 12026 More progress reports when building cache files for ms_peptidesummary with hundreds of thousands of protein hits.
  • 12036 Changes to ms_peptidesummary::findPeptides to support finding error tolerant modifications.
  • 12037 Added ms_mascotoptions::getSpectrumViewerColourSchemeString.
  • 12053 Improved examples for using ms_peptidesummary.
  • 12101 Support for C# under Windows. See C# toolkit installation and Using the toolkit from Perl, Java, Python and C#.
  • 12121 Mascot security doesn’t allow multiple Fasta files to be specified in multiple groups. The ms_security_tasks::addTask function was just adding the first item in the array.
  • 12172 Implement protein inference for both database and library matches. See Spectral libraries.
  • 12173 New mascot.dat configuration values for spectral libraries. Primarily adding a new DATABASE_TYPE.
  • 12174 New mascot.dat Options for library search and compression tool configuration. See ms_mascotoptions::getCompressToolSL.
  • 12212 Fixed index error in ms_mascotoptions::isDefaultTargetFDRPercentage.
  • 12222 The module for HTTP Communication to a Mascot Server could not be used from Perl and the documentation needed improving.
  • 12244 Occasional failure to write session files in cases where the authentication type was IP address or computer name.
  • 12331 Support for Perl 5.20 and 5.22 on Linux.
  • 12232 Chimeric duplicate peptide matches missing from some queries in merged results.
  • 12244 Occasional failure to write session files for IP address and computer name.
  • 12265 matrix_science::ms_http_helper class needs to support https.
  • 12291 Added a new matrix_science::ms_loggingmonitor class.
  • 12349 Extend Percolator calculations to all ranks.
  • 12364 Some Error tolerant search reports junk matches and average threshold score of 0.
  • 12391 Added ms_mascotresults_params.
  • 12405 mzIdentML export of fragment matches fails if ITOL is ppm.
  • 12408 Add XML_SCHEMA_DIRECTORY option to ms_mascotresfile::getXMLschemaFilePath.
  • 12414 Support Python 3.
  • 12428 Create Python scripts for the Parser Documentation.
  • 12430 Score distribution does not include ET matches and the values look wrong.
  • 12431 Support Visual Studio 2015.
  • 12433 matrix_science::ms_http_client now works properly on Linux.
  • 12438 Supply Perl, Python and Java modules built using VS2012 rather VS2005/VS2008. See Installation on Windows, Python toolkit installation, Installation on Windows for details of Visual Studio Runtime Library requirements.
  • 12448 Cache file with missing quantitation if errors due to missing xsd file causes missing quantitation information.
  • 12456 Added an additional bool parameter (addMissingResidueMasses)to the matrix_science::ms_masses constructor that takes a ms_umod_configfile parameter.
  • 12458 Inconsistent handling of whitespace in user parameters between cache and non-cache mode.
  • 12468 Add ms_umod_modification::isSameAs comparison method and ms_umod_modification::getSpecificityBySiteAndPosition.
  • 12497 New overloaded method ms_inputquery::getRetentionTimes for reading all rtinseconds values.
  • 12508 New mascot.dat setting for ions score cutoff checkbox / edit box ms_mascotoptions::getDisplayNonSignificantMatches.
  • 12578 Changes to updateForInstaller for Mascot Server 2.6.
  • 12604 ms_inputquery fails to parse a peak list if it contains no colons.

2.5.2 (21-Nov-2014)

  • 11333 Increase the default value returned by ms_mascotoptions::getPercolatorMinQueries from 100 to 750.
  • 11806 Make getProteinRatio() return negative standard deviation, standard error and p-values when protein ratio type is weighted.
  • 11825 Performance improvements for ms_inputquery.
  • 11856 The function getNumDiscoveredErrTolMods filters was erroneously filtering out some error tolerant peptides and their modifications.
  • 11862 Support filtering of peptides using decimal mass values as doubles rather than strings.
  • 11863 Support UTF-8 in XML configuration files
  • 11883 Add support to ms_ms2quantitation::normaliseIntensities to allow for normalisation to selected peptides or proteins when using summed intensities.
  • 11884 ms_ms2quantitation::getCombinedReportRatioNames now returns unique ratio names in file order rather than alphabetical order.
  • 11885 Misleading warning message for some error tolerant search results where _ignoreiosscorebelow is non-zero.
  • 11888 Support for Visual Studio 2013, Update 3.
  • 11892 Specificity visibility class was not allowing for multiple sites of the same name that differ by position.
  • 11899 ms_umod_modification::findSpecGroup was sorting modification sites incorrectly.
  • 11907 ms_peptidesummary::getQuantitationComponentForPeptide, should exclude a peptide if it matches more than one component.
  • 11959 Performance improvements for ms_mascotresfile::getRepeatSearchString.
  • 11960 Open cache files for writing as soon as possible to reduce potential problems with multiple processes trying to create at the same time.

2.5.1 (17-Jul-2014)

  • 6930 Error tolerant match with exactly the ‘same’ score as a standard match is not discarded.
  • 10671 New function: ms_mascotresults::getQuantitationComponentForPeptide.
  • 11467 Add a new MSPEPSUM flag to specify using homology threshold for ignore ions score below.
  • 11486 Support Perl 5.16 under Windows and Linux, and Perl 5.18 under Linux.
  • 11545 Cron and ExecAfterSearch in mascot.dat cannot cope with spaces in paths.
  • 11547 matrix_science::ms_peptidesummary::getProtein() fails to return null when dbIdx is incorrect.
  • 11622 A residue mass of zero is not permitted in mod_file. It is allowed in a unimod file.
  • 11634 Report standard error as well as standard deviation. Added function: matrix_science::ms_protein_quant_ratio::getStandardError.
  • 11686 Added support for global and per-group modification visibility for matrix_science::ms_umod_configfile.
  • 11705 Improved behaviour for chimeric spectra. New flag: matrix_science::ms_peptidesummary::MSPEPSUM_REMOVE_CHIMERIC_DUPES.
  • 11708 ms_peptide::getAnyMatch was broken and always returned true in version 2.4.4 and version 2.5.0.
  • 11718 Added new functions: getNumDistinctPeptideRepeats and getDistinctPeptide.
  • 11797 ms_datfile::updateForInstaller shouldn’t update parse rules if Database Manager is being used.

2.5.0 (26-Nov-2013)

  • 10290 Added support for HTTP Communication to a Mascot Server.
  • 11234 Move quantitation support from the perl cgi scripts to Mascot Parser.
  • 11235 Added a new function: ms_mascotresults::getProteinEmPAI
  • 11358 When combining results files, need to check that quantitation methods match rather than just comparing names.
  • 11392 Need to be able to return std::string & parameters in Java. SWIG supports returning references to native types in Java by passing a single element array of, for example an int. However, it doesn’t support this for std::string.
  • 11399 Simplify the requirements for specifying the location of the unimod and quantitation schema files when using ms_mascotresfile.
  • 11409 Temporary cdb file created even when MSPEPSUM_DISCARD_RELOADABLE not specified. Minor performance issue, but no other side effects.
  • 11411 Save qmatch and qploghole in the cdb file to improve performance.
  • 11415 ms_mascotresfile now inherits from the ms_errors class.
  • 11422 Under Windows, file sizes stored in cdb files are limited to 32 bits. Larger files had ‘wrapped around’ values and cdb files will be rebuilt automatically for these files.
  • 11425 New function ms_mascotresults::getIonsScore to return an ions score more rapidly than calling ms_mascotresults::getPeptide and then ms_peptide::getIonsScore
  • 11438 The functions ms_mascotresfile::getObservedCharge and ms_mascotresfile::getObservedMrValue need an optional parameter for specifying the summary or decoy summary section.
  • 11513 Save the values returned by ms_protein::getCoverage in the cache.
  • 11568 Remove support for Mascot Integra
  • 11631 Sign the msparser.jar file using a CA trusted certificate

2.4.4 (4-Nov-2013)

  • 10873: Support Python 2.7
  • 11559: Add MISECTASK_ flags for Mascot Insight to the security_tasks.xml file
  • 11560: MSPEPSUM_DISCARD_RELOADABLE and MSRES_INTEGRATED_ERR_TOL are incompatible.

2.4.3 (1-Oct-2012)

  • 11115: Provide interface to the tree/hierarchical cluster method of the C Clustering library: ms_treecluster.
  • 11126: New function: ms_mascotresfile::getNumEtSeqsSearched().
  • 11190: The function getProteinTaxonomyIDs() now also returns taxonomy IDs for PMF results where they are available for Mascot 2.4.1 and later. In version 2.4.0, it only returned values from the proteins section (for ms-ms searches).
  • 11269: Incorrect return value for getObservedCharge() when the charge state is greater than 8+.
  • 11275: Additional return values for getThresholdForFDRAboveIdentity() and getThresholdForFDRAboveHomology()
  • 11305: Error: "Requested query 1, hit -64 in function ms_proteinsummary::getPeptide" with some PMF mixture results when creating a ms_proteinsummary

2.4.2 (27-Jul-2012)

  • 11182: Support streaming of compression data using ms_zip.
  • 11185: Support for multiple modifications on one site in ms_aahelper.
  • 11201: ms_aahelper constructor using a results file also needs to supply a path to the unimod schema and should report errors when the schema cannot be found.

2.4.1 (23-Apr-2012)

  • 10471: Added functions: matrix_science::ms_datfile::getHeaderComments matrix_science::ms_datfile::setHeaderComments matrix_science::ms_customproperty::getPreceedingComments matrix_science::ms_customproperty::setPreceedingComments
  • 10797: Added functions to save and load custom parameters for ms_group and ms_user. See: matrix_science::ms_group::saveStringParam and matrix_science::ms_user::saveStringParam
  • 10798: New functions matrix_science::ms_mascotoptions::getReportBuilderColumnArrangement and matrix_science::ms_mascotoptions::setReportBuilderColumnArrangement
  • 10823: New function matrix_science::ms_peptide::getSummedModsStr for improved support in Mascot 2.4 for modifications on labelled residues. See also Multiple modifications for the same site
  • 10874: New function matrix_science::ms_taxonomyrules::getSpeciesFormatRegex() for additional regular expression in the Taxonomy_n section to read speclist.txt
  • 10906: New function matrix_science::ms_mascotresults::getThresholdForFDRAboveIdentity returns false and fails to find reasonable values for some Percolator files
  • 10943: Cron emulator improvements including new ms_cronoptions functions: getLoggingLevel(), setLoggingLevel(), getLogFileName() , setLogFileName() , deleteCronJob() and setCronJob() and new ms_cronjob functions: isEnabled() and setEnabled()
  • 10979: Add support for RAWFILE and LOCUS to matrix_science::ms_inputquery
  • 10991: matrix_science::ms_mascotresfile::versionGreaterOrEqual returns incorrect value.
  • 10995: Internal change to allowed values for identity threshold.
  • 11002: Change minPepLenInPepSummary functionality. Don’t show proteins in which the only significant peptides have length < MinPepLenInPepSummary.
  • 11018: matrix_science::ms_mascotresults::getThresholdForFDRAboveIdentity and matrix_science::ms_mascotresults::getThresholdForFDRAboveHomology can fail to get the best values.
  • 11042: matrix_science::ms_mascotresfile doesn’t fail safely if a cache file cannot be created due to incorrect permissions. Issue was introduced when Bug 10745 was fixed in version 2.4.0.
  • 11041: On 64 bit Linux only, the function matrix_science::int ms_mascotresults::getQmatch() can return a ‘wrapped’ negative number in the extremely rare case of the qmatch_x= value being > INT_MAX. In such cases, it now returns INT_MAX on all platforms.
  • 11094: Using matrix_science::ms_peptidesummary::MSPEPSUM_NO_PROTEIN_GROUPING can cause a crash when creating a ms_peptidesummary object.

2.4.0 (11-Aug-2011)

  • 10536: IgnoreIonsScoreBelow is converted to a score and rounded to an integer internally. First fixed as bug #567 in version 2.3, but this minor issue was re-introduced in version 2.3.1
  • 10610: "Possible duplicate accession string" errors caused by two accessions that only differ in upper/lower case.
  • 10611: Memory efficient mode for large search results. See matrix_science::ms_peptidesummary::freeHit and matrix_science::ms_peptidesummary::MSPEPSUM_DISCARD_RELOADABLE
  • 10621: Added new class: matrix_science::ms_taxonomytree and function: matrix_science::ms_mascotresults::getProteinTaxonomyIDs to support additional taxonomy information available in Mascot 2.4 and later.
  • 10622: Added functions matrix_science::ms_mascotresults::createSummary, matrix_science::ms_mascotresults::getCreateSummaryProgress and matrix_science::ms_mascotresults::cancelCreateSummary to enable an application to cancel creating an ms_peptidesummary object.
  • 10623: Confusing error messages if ExecAfterSearch logging level set incorrectly.
  • 10624: Increase 2Gb CDB file size limit to 4Gb for 32 bit applications.
  • 10626: Font size in chm (help) file is too large.
  • 10627: On Windows, NTFS, cache files get re-created when going to/from daylight savings. Cache directory names also change.
  • 10628: New function: matrix_science::ms_mascotresfile::resetKeepAlive and added a %f tag for displaying the filename, which is useful with Combining multiple .dat files
  • 10629: Small memory leak in protein family grouping.
  • 10630: New function: matrix_science::ms_connection_settings::setUserAgent() and matrix_science::ms_connection_settings::getUserAgent()
  • 10631: Rare crash when using results cache with family summary and minPepLenInSearch < minPepLenInPepSummary.
  • 10632: ms_protein copy constructor is not reliable when using the results cache
  • 10634: ms_protein copy constructor is not reliable when using the results cache
  • 10652: Cannot load protein description line from ms_mascotresfile when protein accessions contain an = sign.
  • 10657: matrix_science::ms_peptide::getProteins() can return incomplete list when lead protein in a family is not the highest scoring.
  • 10668: Added function matrix_science::ms_mascotresfile::getMultiFileQueryNumber useful with Combining multiple .dat files
  • 10673: Added function matrix_science::ms_mascotresults::findProteins and added flags for searching for modifications.
  • 10682: Added functions: matrix_science::ms_mascotoptions::setIgnoreDupeAccession() and matrix_science::ms_mascotoptions::setReportNumberChoice()
  • 10704: Add support for a taxonomy rule where TaxID explicitly given.
  • 10711: Make ms_tinycdb thread safe.
  • 10711: Add a method to ms_session to return the timeout value.
  • 10734: Use only the filename part of result files when constructing the cache filename for a multi-file peptide summary.
  • 10745: Creating an ms_mascotresfile object with a ‘junk’ file when specifying RESFILE_USE_CACHE creates a (tiny) cache file. The second time the ms_mascotresfile object is created with the same parameters, it reads the tiny cache file but fails to set the INVALID_RESFILE error.
  • 10749: matrix_science::ms_mascotresfile::getNumQueries() incorrectly returned -1 for the last file in a multi-file result set.
  • 10780: Change definition of matrix_science::ms_mascotresults::isPeptideUnique to be unique per family member rather than per family.
  • 10804: Change matrix_science::ms_mascotresults::getPeptideThreshold() to allow return of either homology or identity threshold as double.

2.3.3 (11-Oct-2010)

  • 461: ms_umod_configfile::getElementByName() hangs if called with null argument. Now just returns NULL
  • 596: Documentation improvements and restructuring of some of the help.
  • 614: ms_aahelper::createPeptide now supports more than 9 variable modifications.
  • 629: Added ms_peptidesummary::FC_SEARCH_ALL_RANKS for use with ms_peptidesummary::findPeptides
  • 630: Accession strings with spaces in are truncated when loading proteins from cache.
  • 632: Added new function ms_peptidesummary::getFlags2()
  • 633: MinPepLenInPepSummary now used for family grouping. Also added function ms_peptide::getPeptideLength.
  • 634: ms_datfile error message says that ‘mascot.dat. file does not exist even when opening file with different name, for example ‘not.mascot.dat’. Change message to output the name of the file.
  • 635: Added support for Combining multiple .dat files.
  • 638: ms_mascotresfile::getRepeatSearchString does not include scans, rawscans, rtinseconds and index.
  • 639: Added ms_mascotresfile::enumerateQuerySectionKeys
  • 641: Unigene reports too slow. A cache file is now created and used automatically.
  • 644: Added tags to pass through session_id and task_id in ms_mascotoptions::getExecAfterSearch
  • 645: Can’t load family report for an ET search with ignoreIonsScoreBelow >0 and < 1
  • 647: Add Support for Python under Linux.
  • 649: Performance improvements for ms_mascotresults::getProteinDescription and ms_mascotresults::getProteinMass.
  • 653: Very slow to create cache files when > 100k potential proteins in the results file.
  • 654: Concurrency issue on Windows when using ms_session.
  • 655: ms_fragment::getLabel returns an string with a truncated rather than a rounded neutral loss. For MetOx, this reports -63 rather than -64.
  • 656: Concurrency issue: if two processes try to create a directory using ms_fileutilities::createDirectory at the same time, one process may fail.

2.3.2 (11-May-2010)

  • 624: Family grouping no longer requires that the top scoring protein for a group appears as a lead protein. There are cases where more compact grouping can be obtained by making the highest scoring protein a subset/intersection.
  • 626: In rare cases, a protein could be marked as a subset when it should have been another family member. This is because the algorithm defined a protein as a subset when all of the peptides were found in any other protein, rather than any other family member protein.
  • 627: Change to ms_aahelper::ms_aahelper constructor when creating from a ms_mascotresfile. Added an additional optional parameter to pass a quantitation schema that will be used before calling ms_mascotresfile::getQuantitation
  • 628: Functions ms_protein::getNumDisplayPeptides and ms_protein::getNumDistinctPeptides return incorrect values for an error tolerant search when the flag for aboveThreshold is set to true. Error tolerant matches are now ignored in this case.

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 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 documented 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 algorithm 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 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 suppress 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 procedures 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 multiple 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 ambiguous 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 hierarchy 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 accession 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