最初にお読みください（Mascot Server version 2.7.0 Windows 版）

1

最初にお読みください
Mascot Server version 2.7 for Windows Release Notes
新規インストール
新規インストールを行う前に、2頁の「最新の追加情報」に対応する注意点」をご覧ください。
イ ン ス ト ー ル DVD に あ る 「 Mascot_Server_v2.7_Win_ 新 規 イ ン ス ト ー ル 手 順 .pdf 」 書 類 に し た が っ てインストールを進めてください。また、インストールDVDにある「manual.pdf」書類の「3. Installation:Windows」も併せてご覧ください。

アップグレードバ ー ジ ョ ン 2.6 か ら バ ー ジ ョ ン 2.7 に ア ッ プ グ レ ー ド す る 場 合 は 、 イ ン ス ト ー ル DVD に あ る「Mascot_Server_v2.7_Win_アップグレード手順.pdf」書類にしたがってアップグレードを進めてください。
また、インストールDVDにある「manual.pdf」の「3. Installation: Windows」も併せてご覧ください。
なお、今まで使用していたライセンスファイルはバージョン2.7では使えませんので、弊社が提供するプロダクトキーを使ってバージョン2.7用のライセンスファイルを新規に取得してください。

新規サポート機能
インストールDVDにある別紙資料「ver.2.7新機能紹介.pdf」をご覧ください。

バージョン 2.6 からの変更点
3頁にバージョン2.6.0 からの変更点をまとめました。なお、この書類以降に追加された内容を含む最新の変更点に関しては、2ページの「最新の追加情報」並びに「http://www.matrixscience.com/mascot_support_v2_7.html」をご覧ください。

最初にお読みください（Mascot Server version 2.7.0 Windows 版）

2-----------------------

最新の追加情報----------------------お客様が作成したPerlスクリプトやサードパーティのプログラムに対するヘルパー・スクリプトがMascotフォルダにインストールされている場合、それらのスクリプトがMASCOT のセキュリティ設定が適用されないセキュリティホールになる可能性があります。MASCOTのセキュリティ機能をご利用の場
合はご注意ください。

最初にお読みください（Mascot Server version 2.7.0 Windows 版）

3------------------------------------------

バージョン 2.6.2 からの変更点-----------------------------------------以下の表並びに http://www.matrixscience.com/mascot_support_v2_7.html をご覧ください。また、下記項目の「Description」はメモ書きのような記述内容です。内容が気になる項目の詳細については弊社までお問い合わせください。

ID4701
6036
6289
6529
6563

Component

ServerServer
ServerServerServer

6762 Server6795 Server
6897
10427
10714
10793

ServerParser
ParserParser10932 Server
11283 Server
11515 Server
11802 Parser
11821 Server
11835 Server
11930 Server
12139 Server
12148 Server
12190 Server
12326 Parser
12365 Server
12393 Server
12397 Server
12399 Server
12420 Server
12482 Daemon
12496 Parser

Description
Support third column in mgf fragment ion list for charge state
Variable mods permutations limit needs rethink
Can't open for "reading". Error No such file or directory [M00012]
Report decoy stats for proteins as well as peptides
Monitor very slow to start up under Windows when there are a large number offiles under data
Cannot have both fixed and variable mods with terminus specificity
Get incorrect deltas if fixed and variable mods have overlapping but notidentical specificity'Silly' search causes crash in cluster mode. OK in standalone mode
ms_aahelper needs argument to generate mass values for all neutral losses
Parser error handling is not thread safe
findPeptides() with FT_PEPTIDE_EXP_MZ and FC_SEARCH_ALL_RANKS returns
all ranks with no match
Change to Trypsin if Manual error tolerant run
symlinks are deleted by the installer. For example, if you have setc:¥inetpub¥mascot¥data => d:¥mascot_data
Quantitation checkboxes enabled when related information can not begenerated
Python example script emits "query out of range" errors and crashes
Display long accessions in fullShow ET mod delta in modification counts, refine the yellow popup and allow
searching for ET mods by delta
Add a confirmation button for deleting users and groups
When exporting percolated results with retention times enabled, the export
form should not try to percolate the results a second time
Add switch to mascot.dat to over-ride asynchronous search submission (batchmode)
Add a checkbox to the MGF export form that outputs spectra in the originalorder
Add switch to mascot.dat to over-ride asynchronous search submission (batchmode)
Failing to escape "&" in MS_STATUSXML
SwissProt PMF uses frightening amount of RAM
SVG spectrum graphic scales intensity axis incorrectly when match has reporter
ions
SwissProt is not online; pI and sequence coverage are not available.
Inconsistencies in use of lower case letters for collapsed /alternative matches
Add a link for the combined search resultsDisallow creating a database whose name differs from an existing one only bycase最初にお読みください（Mascot Server version 2.7.0 Windows 版）

12504
12515
12523
12575
12610
12616
12617
12620

ServerServer
ServerServerServerDaemonDaemonServer

12633
12634
12646
12667
12697
12701
12705
12714
12730
12753

ServerServerServerServerServerServerServerServerDaemonParser12768 Server
12769 Server
12770
12805
12806
12811

ServerServerServerServer

12812 Server
12813 Daemon
12822 Server
12834 Server
12842 Server
12843
12847
12857
12860

ServerServer
ParserParser12863 Parser
12865 Server
12869
12875
12888
12890
12895

ServerDaemonParserServerParser4

Cleavage sites in spectrum graphic labelled incorrectly
Add Fasta to export formats
Display the number of active / inactive databases.
Modifying the fasta or msp file results in deletion of the old file
Forward all non-fatal error messages from cluster nodes back to master
Prevent submitting a library search as PMF or error tolerant or as average mass
Task never completes with certain follow-up settings
Mods defined in a quantitation method are not imported correctly in a spectral
library
http://maxquant.org/contaminants.zip is no longer there
Fails to recognise downloaded file is compressed
Roll-up of changes to Manual, release notes, and HTML pages for 2.7
SearchControl very slow to create cache files
Error 587: Inconsistent peptide length : 6 provided, 5 in use
Protein Family Summary should support tag searches
Quantitation module of configuration editor is using old schemaTime to drop extract_msn search form
Checkboxes in auto-export dialog all checked on load
ms_tinycdb openIndexFile uses string comparison on gmt timestamps to checkfile dates
Need to check at start of search that all query level mods are valid
Database Manager log files (e.g. db_manager.log) use UTC, while other Mascot
logs use local time
Reporting of MIME errors in input file not working correctly
Windows installer does not backup fragmentation_rules, but does overwrite it
Crawled MSP file's comment field "File" should use forward slashes on Windows
Top down ET search with one significant first pass sequence shows no matches
when trying to display ET results
Windows 8.1 and Windows 10 Start menu does not support subfolders. So, for example, the 'admin' or 'Distiller' folders are not shown.
Windows 10 (and possibly 8) Start menu does not appear to have sub folders.
So, for example no 'admin' or 'Distiller' folders
If m_queries is higher than SplitNumberOfQueries in PMF, stop the search andwarn the user
Export of a library-only search shows default threshold of 0.05 instead of 300
Error when adding frame number to an accession for ms-getseq inpost request
Mascot Daemon does not report the top hit for a Spectral library search
Suppress PSMs with complementary deltas in error tolerant searches
Potential crash when sorting peptides
willCreateCache adds errors to the ms_mascotresfile object, resulting in
duplicates
Search modification by name with findPeptides returns only one value onWindows
Missing or outdated b00 file should trigger a recompression like other index
files
Increase number of download attempts
Review string encoding in Daemon when submitting searches as POST requests
Add a documentation page for the FDR procedure
programming error when filtering on Mr(calc)
Add a utility function to compare XML files

最初にお読みください（Mascot Server version 2.7.0 Windows 版）

12899
12900
12902
12906

ServerServer
ParserServer12913 Parser
12921 Parser
12924 Parser
12933 Server
12936 Parser
12937 Parser
12972 Server
12977 Parser
12985 Daemon
12987 Daemon
12990 Parser
12997
13003
13020
13029
13032
13033

ServerServer
ParserParserServerParser

13034 Server
13043
13045
13046
13058
13063
13065
13075
13086
13088
13091

ServerServerServerServerServerServerServerServerServerServer

13094
13101
13102
13108
13109

ServerParser
ServerParser
Server13118 Server

5

Result files for searches against a single fasta should not have qX_pX_db lines
Add protein mass and peptide missed cleavages to mzTab output
Modification statistics for error tolerant search can be highly misleading
Warning: unexpected difference between Mr from result file (1992.829956) andMr re-calculated from masses (1990.835879425)
Revert to just saving rank 1 in percolator pip file
Add PSM and sequences used for ID to proteinHit element of quant XML export
Peptide summary cache file name is different between master_results andms-searchcontrol
On monitor start-up, if the reference fasta is incorrectly cased, warn that asimilar database exists
Report of Error tolerant search does not display all matches when None isselected
Update from SWIG 2.0.12 to SWIG 3.0.12 for ALL languages supported by Parser
Substitution of XBZ is not consistent at either terminus - Erroneous absence ofbraces in CSeqModifier::chooseNextRes
Revive MinGW as target platform and compile against ActivePerl/Strawberry
Perl 5.26, 5.28, 5.30
Should be some easy way to open the parameter set selected in task editor tabin the parameter editor(MDS1016) 5: Nullable object must have a value
Logging: Improvements for ms_ms_loggingmonitor required including better
documentation
Cannot create custom annotation URL for NA database
Isn't numeric in sort error message when crawling and building a SL.
I don't believe PSM and PepSeq counts for Percolated results
Add ActivePerl 5.24, 5.26, 5.28, 5.30 build targets on Linux
Cross-link changes in nph-mascot.MSP File Format Issues (Was Error message text for
ERR_MSP_NIST_MSP_NO_SPECTRA is misleading)Put all warnings and errors from parsing a spectral library into the compressionlogMust click Next twice when copying a database definition
Tooltip on FDR says 'False decoy rate'
Search form changes for intact crosslinking
Remove CMC as mail option
DBM error after installation
Percolator is executed by default for all auto-decoy searches
Need an option to suppress pip file creation
Feature finder outputs z+2 fragments as z+1 fragments
Bug in copying over or replacing PRIDE_Contaminants?
When using DECOY_PROTEIN_RANDOM as DecoyTypeNoEnzyme, no peptide
matches in a 5-sequence AA database
Incorrect insertion of forward slash in a file URL if directory doesn't exist
Add support for Python 3.6
Tag searches should not allow ambiguity codes.MSP File Format Issues #2
Error tolerant wierdness with lower case peptide sequences, peptides assigned
to the wrong protein and scoring differences
Search for a variable mod in the report, subset protein link is sometimes faulty最初にお読みください（Mascot Server version 2.7.0 Windows 版）

13122 Parser
13124 Parser
13131 Server
13132 Server
13133 Server
13140 Server
13144
13149
13154
13164

ServerServer
ServerServer

13168
13169
13172
13200

ServerServerServer
Parser13208
1320913221
13222
13226

ServerServer
ServerDaemonServer13227 Server
13230 Parser
13234 Parser
13241 Parser
13243
13244
13245
13250
13251
13268
13272
13274
13275
13276

ParserServerServer
DaemonServerParserServerServerServerParser

13284
13288
13295
13296
13297
13298
13301
13310

ParserParserServerServerServerServerParserParser6

Mascot Server reporters error with ms-ms data when variable reporter ion
modifications are selected
Segfault when caching an iTRAQ 4-plex file with variable mod group
Checkboxes for optional columns become enabled after going back in browser
history
Proxy authentication fails for HTTPS requests tunneled through an HTTP proxy
Display crosslinked peptides in Peptide View
New command for ms-status.exe for checking when configuration files havebeen synched with nodes
Modifications module of configuration Editor needs to support crosslinkers
Search with query level IT_Mods crashes
Add a message to monitor.log to say a node has been started/shut down
Platform-dependent rounding differences in generated spectral library and data
exported with export_dat_2.pl
Test harness changes to unimod.xml and unimod_xl.xml
Crash when running a search with less queries than nodes
Remove upper limit on MinPepLenInPeptideSummary
New ms_peptidesummary constructor parameter: minimum number ofsignificant unique sequences
Format time in a standard way in the stats file
Monitor crashes on linux with an old glibc in a sequence is too long
Still problems if fixed and variable mods have overlapping specificities
Limit number of cores or threads Mascot Daemon uses for processing.
In Peptide View, link for lower ranking peptides is missing_minpeplen
Add an ion mobility field to MGF
ms_mascotresfile::appendResfile() generates lots of XML errors unless used on
Mascot Server
Crosslinking method definition API and class structure
Description of getMaxPepModArrangements method in the documentation isconfusing
Update unimod.xml to the latest one
Merge master_xl.xml and usermod_xl.xml to unimod_xl.xml
Add crosslinking.xml and crosslinking_1.xsd to the shipper image
If the PeakListRoot registry value is invalid, Daemon won't start
Modification statistics depend on setting of 'Max. number of families'
ms_peptidesummary::isDataCached() returns false for BUGFIX_12740
Display crosslinked peptides in Protein View
Read crosslinking parameters from crosslinking.xml
Read crosslinkers from unimod_xl.xml
ms_mascotresfile::getMasses() sets electron mass to 0.0 for results files from
1.9 and earlier
DEFAULT_MINPEPLENINPEPSUMMARY should be 7
ms_fragment needs a constructor for precursor NL peaks
Pretty print crosslinking method and linker definition
get_params.pl: Output [LINKERS] and [CROSSLINKING] sections
MGF export for mzIdentML should specify correct file nameSuppress or remove lastquery.mgf
Add flanking residues to the distiller xml MS1 quantitation results export
Peptide without required fixed mod for Reporter quant incorrectly has quantratios

最初にお読みください（Mascot Server version 2.7.0 Windows 版）

13312 Parser
13313
13315
13316
13322
13324

ServerParser
ServerDaemonParser13326 Server
13329 Server
13337 Parser
13351 Server
13370
13372
13383
13393
13408
13409

DaemonServerServer
ServerDaemonParser

13411
13420
13437
13445

ServerServer
ParserServer13455 Server

7Add new option in ms_mascotoptions for suppressing PIP file creation during
the search
New command to ms-status.exe, MS_CROSSLINKINGXML_COMPRESSED
Review default crosslinking methods in crosslinking.xml
Update SwissProt and PRIDE_Contaminants for the installer
Mascot Daemon seq-database field length is to small
New method ms_mascotresults::getDiscoveredLocalModDeltas(), and output
order of getDiscoveredErrTolModDeltas() is ambiguous
Add text to the installer to make it clear that it's easier to use IIS on Windows
ms-config.exe needs to pretty print the crosslinking method"The msp file: '%s' contains a spectrum with no peaks" should be a warning, notan error
Matches with scores below 0.001 should not appear as they are
0.00 in the result files
Perseus / CSV quantitation export
Report percentage progress when exporting merged results
Add function to client.pl to return quantitation.xml config file
Add a new TMT 16-plex quantitation method
Add crosslinking to parameter set
ms_peptide::getIonsScore() and ms_mascoresults::getIonsScore() return
different values with same args.
Basic configuration editor for crosslinking methods
MSPepsearch magically changes CAM -> Carbamidomethyl
Add Options: DechargeFragmentPeaks
The reference cdb file of a spectral library is not updated when the reference
database is updated
Change the default MaxSequenceLen to 80000

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