最初にお読みください（Mascot Server version 2.8.0 Windows 版）

1

最初にお読みください
Mascot Server version 2.8 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」をご覧ください。インストールDVDにある「Mascot_Server_v2.8_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 2.7 か ら バ ー ジ ョ ン 2.8 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_v2.8_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2.8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.2.8新機能紹介.pdf」をご覧ください。

バージョン 2.7 からの変更点
3頁にバージョン2.7.0 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頁の「最新の追加情報」並びに「https://www.matrixscience.com/mascot_support_v2_8.html」をご覧ください。

最初にお読みください（Mascot Server version 2.8.0 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 2.8.0 Windows 版）

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

バージョン 2.7.0 からの変更点-----------------------------------------以下の表並びに https://www.matrixscience.com/mascot_support_v2_8.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。
Component

ID
5326
10897
11120
11198
11228
11917
12002

ServerServer
ServerServerServerServerServer

12447
12552
12559
12628
12666
12790

ParserServerServerServer
ServerServer

12843 Server
12870
12969
13000
13019
13084
13129
13224
13317
13325

ServerParser
ServerServerServerServerServerServerServer13357 Parser
13378 Parser
13381 Server
13386 Server
13391
13396
13404
13406

ServerServer
ServerParser

13407
13424
13431
13434

ServerServer
ServerServerDescription
Remove the "MonitorTestTimeout" value
Modernise browser.pl
Number of entries searched in error tolerant mode is incorrect
Use decoy results to set FDR automatically
Make ms-createpip.exe multithreaded
Error tolerant decoy search using fusion decoy database
We should change the interpretation of REPORT for summaries otherthan family
Calculate an expect value for error tolerant matchesmzTab glitches prevent PRIDE submission as complete submission
et_sequences set to a wrong total in cluster split by query
Perl relocation path has double slash
XML export fails to validate against mascot_search_results_2.xsd
ms-monitor.exe should bring fasta files with valid compressed files
online first
Mascot Daemon does not report the top hit for a Spectral library
searchSign the installer
Documentation changes roll up for msparser 2.8
Followup search fails to filter out matches from SL search.
CentOS 7: install1.pl says "Can't locate strict.pm: permission denied"Getting more from Percolator
Remove browser.plFlaw in email verification on pubwww4
Full configuration editor for crosslinking methods
If SwissProt fails to compress, PRIDE_Contaminants prevents otherdatabases from compressing
Announce end of 32-bit Parser on Windows
Section title "Using STL classes" should mention vectord, vectori,
VectorString
Export doesn't fully support pepseq-based FDR
ms-status.exe doesn't accept a Mascot security session ID as acommand line argument
Use OpenMP acceleration with PercolatorExport crosslinked matches in CSV and XML format
Remove maximum protein limit on intralinked searches
getThresholdForFDRAboveIdentity() doesn't always work when
Percolator is enabled
Possible bug with double downloading of databases_1.xml
Different Percolator results in Windows vs Linux
Save the build date in Mascot binaries
Changing only numbers in the XML of a quantitation method does not最初にお読みください（Mascot Server version 2.8.0 Windows 版）

13470 Server
13475 Server
13476 Server
13477 Daemon
13491 Server
13501
13508
13512
13514
13515
13522
13523
13528
13533

ServerServerServerParser
ServerServerServer
ServerServer

13536 Server
13537 Server
13538 Parser
13540 Server
13541
13542
13543
13544

ServerServer
ServerServer

13550 Server
13552 Server
13553 Server
13559 Server
13564 Server
13566 Server
13568 Server
13586 Server
13590
13592
13595
13600
13601

ServerServer
DaemonServerServer4

update it
Mascot Daemon does not report the protein description and protein
mass for top hit for a Spectral library search
Product licensing POST request should use HTTPSMultithread crosslink searches where number of accessions is fewer
than number of available threads
Save as dialog when generating a quantitation summary export canappear behind window
When reference database of a spectral library is not online,
ms-monitor.exe outputs 60 log messages every minuteCompile Mascot 2.8 with GCC 7
Remove the limit from linker arrangements
Crawled library compression warns about "2-succinyl (C"Parser 2.7.0 C# is built with VS2015, not VS2012
Confirm TLS1.2 is supported for database downloads
install1.pl stops with msparser version error
Remove hardcoded msparser version check from install1.plHTML footer of help pages says "Copyright 2016"
Optimise preprocessing and distribution of peak lists at the start ofthe search and within a chunk
Overflow checking is incorrect in add_with_no_overflow()
Allow ET + decoy to be selected in the search form
Calculate FDR for ET decoy search in
getThresholdForFDRAboveHomology()
Only search unassigned/unmatched queries in second pass of ETsearchProtein selection in ET search could be based on target FDR
Protein Family Summary: display expect value for ET matches
Display FDR for ET decoy searches
Mascot 2.7 executables on Linux fail to work on certain AMD Opteron
CPUs
Library import fails if start date left at default of --start-date1970-01-01
Roll-up of changes to Manual, release notes, and HTML pages for 2.8
ms-getseq.exe fails to escape protein reference text;
ms-gettaxonomy.exe prints an invalid ending tag in accession lookup
mode
ms-gettaxonomy ignores ACCESSION parameter when TAXID ispresentxiVIEW CSV export fails to encode fixed mods
Configuration Editor writes empty code and pairs_with attributes
Search gives incorrect results when taxonomy filter specified anddatabase update has stalled
Incorrect protein accessions in result file when in cluster mode,
searching multiple databases and last database is smaller than theothers
Ion mobility MGF field documentation is incorrect
Deactivate neXtProt and it cannot be activated again
Display database details as part of version update warning
Percolator flags can be incorrect when executed by ExecAfterSearch
Progress bar allocation for ms-createpip and Percolator should be
50:50

最初にお読みください（Mascot Server version 2.8.0 Windows 版）

13602
13604
13605
13609
13618
13624

ServerParser
DaemonServerServerServer

13628 Server
13633 Parser13634 Parser
13638 Server
13639
13652
13653
13660
13661
13662
13663
13664
13665
13666

ParserServerServerServer
ServerServer
ParserDaemonDaemonServer13668 Server
13673
13676
13679
13696
13703

ParserServerDaemon
ParserServer13709 Server
13714 Server
13715 Parser
13724 Server
13726 Parser
13729 Server
13730 Parser
13732 Server
13734 Server
13746 Parser
13750 Server
13752 Server
13753 Server

5

Update Percolator sources to 3.05
New setting for number of input file parsing threads
Cannot toggle individual checkboxes of sample map
Occasional segfault on cluster node on Windows
Cannot export Fasta on pubwww4
Rare false positive disulfide bridge looplink match, caused by applying
doubled linker mass to calculated precursor massmzIdentML takes forever with this file
updateForInstaller: replace PercolatorFeatures with new feature set
New options PercolatorTargetRankScoreThreshold andPercolatorTargetRankRelativeThreshold
Bundle VC++ 2012 and VC++ 2015-2019 redistributables with Mascot
installer
Compile Parser 2.8 with VS2017
Add back ExecAfterSearch for ms-createpip.exe
Allow Get me to 1% FDR when Percolator is enabledCompile Mascot 2.8 with VS2017
Instruments internal fragment size setting not used in searchmzIdentML export does not include internal ions over 700Da
ms_aahelper never returns internal ions over 700 Da
Allow ET + decoy to be selected in search parameters
Extend the autoexport to export a merged result
Protein FDR reported incorrectly in CSV, XML, mzIdentML, mzTabexport
Exported MGF reports outputs charge state as precursor intensity,plus incorrect charge state ambiguity handling
ms_proteinsummary needs to check inference flags
Ignore SplitDataFileSize parameter in nph-mascotUpdate MS Inc address in Daemon help
New parameter for ms-createpip.exe multithreading
Update SwissProt, PRIDE_contaminants and taxonomy files inshipper package for 2.8
Use TARGET_FDR_PERCENT= at end of target-decoy search andwrite sigthreshold as first_pass_threshold=Protein Family Summary should be the default report
Only return false from getThresholdForFDRAboveHomology() ifclosest FDR is not within a factor of 2 of target FDR
Unnecessary work when modifications with 0 instances have samespecificity
Logging and error handling documentation is mostly missing
Precursor mass in results file can be wrong when match has looplinks
Allow zero child elements in mxm:accessions, mxm:filters, mxm:scope,mxm:settings
percolate_rt doesn't work
Update example ET search (F981130.dat) and remove obsolete
searches F981126.dat, F981127.dat, F981128.dat
Remove ICC2016 shippers, add GCC7 internal shippers
Move target FDR selection into format controls
If the crosslinking method cannot be written, stop the search
immediately
In cluster split by query, add the warnings from the master to theresult file最初にお読みください（Mascot Server version 2.8.0 Windows 版）

13757 Server13759
13761
13762
13763

ParserServerServerParser

13769 Parser
13787 Server13790 Server13803 Server
13806 Parser
13808 Parser
13818 Parser
13821 Server
13848 Parser

6Warnings from the error tolerant and crosslink pass are not added tothe files
New ms_peptidesummary parameters: target FDR and FDR type
Should looplinks count as +2 towards MaxPepNumModifiedSites?
Replace ActivePerl with own version of Perl
Add willCreateCache methods which take ams_mascotresults_params argument
Update unimod.xml and unimod_xl.xml for 2.8.0
Missing crosslink match to a peptide pair with the same complete
string as another match
mascot_search_results_2.xsd fails to compile with xmllint
Replace $Config{perlpath} with $^X in Database Manager
Target FDR algorithm: maximise the number of target matches if FDR
is 0%
Update element descriptions in crosslinking schema for thecrosslinking configuration editor
If alpha and beta are in different proteins, one of them is not assigned
to any protein
Precursor mass in results file can be wrong when monolink index > 9Add Parser targets for Perl 5.32 and 5.34

何かお困りのことがありましたら support-jp@matrixscience.com （技術サポート）にご連絡ください。

マトリックスサイエンス株式会社
電子メール：support-jp@matrixscience.com
電話：03-5807-7895
ファクシミリ：03-5807-7896
住所：〒110-0015 東京都台東区東上野１-6-10 ART ビル１階