最初にお読みください（Mascot Server version 2.5 (2.5.1) Windows 版）

1

最初にお読みください
Mascot Server version 2.5 for Windows Release Notes
新規インストール
インストールを行う前に、2頁の「最新の追加情報」及び3頁の「Windows OS の各バージョンに対応する注意点」をご覧ください。インストールDVDにある「Mascot_Server_v2.5_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」の「3章Installation: Microsoft Windows」も併せてご覧ください。

バージョンアップ前のバージョン(バージョン2.4 及びそれ以前)からバージョン2.5 にバージョンアップする場合は、インストールDVDにある「Mascot_Server_v2.5_バージョンアップ手順.pdf」書類にしたがってバージョンアップを進めてください。また、インストールDVDにある「manual.pdf」の「3章 Installation: Microsoft Windows」も併せてご覧ください。なお、バージョン2.5では弊社が提供するプロダクトキーを使って新規にライセンスファイルを取得する必要があります。

新規サポート機能1. 混合スペクトル（Chimeric spectra）への対応
ひとつのプロダクトイオンマススペクトルデータに複数のペプチド由来のデータが混合しているデータの検索が可能となりました。mgfファイルの中にプリカーサイオンの質量に関する情報を複数与えてMascot検索を実行することができます。

2. 新規スペクトルビュアーのサポート
色分け表示がカーソルの動きに合わせてインタラクティブに変化するほか、SVG形式による出力にも対応しました。

3. その他
・入力ファイルのダウンロードに対応
・64bit版のMascot Daemonの追加
・修飾解析結果のサマリー表示
・Webページのレイアウト変更

バージョン 2.4 からの変更点
4 頁 に バ ー ジ ョ ン 2.4.00 か ら の 変 更 点 を ま と め ま し た 。 な お 、 最 新 の 変 更 点 に 関 し て は 、「http://www.matrixscience.com/mascot_support_v2_5.html」をご覧ください。

最新の追加情報
2頁をご覧ください。

最初にお読みください（Mascot Server version 2.5 (2.5.1) Windows 版）

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

最新の追加情報----------------------(1) Mascot Server に関連して動作するサードパーティのプログラムの中にはヘルパースクリプトを必要とするものがあります。Mascot Server のセキュリティ機能が動作している状態では、これらのヘルパースクリプトがセキュリティホールになる可能性があります。
(2) Microsoft Internet Explorer 8 で使われているファイルアップロードコントロールはテキストのペースト機能をサポートしていません。これにより、Mascot 検索条件設定画面と連動するサードパーテ
ィのプログラム動作に不具合が生じることがあります。プログラムを修正するか、Microsoft InternetExplorer 7 にダウングレードすることで回避できることがあります。

最初にお読みください（Mascot Server version 2.5 (2.5.1) Windows 版）--------------------------------------------------------

Windows OS の各バージョンに対応する注意点-------------------------------------------------------特記事項はありません。

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最初にお読みください（Mascot Server version 2.5 (2.5.1) Windows 版）

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バージョン 2.4.00 からの変更点-----------------------------------------次の表ならびに http://www.matrixscience.com/mascot_support_v2_5.html をご覧ください。

管理番号4719
5768
58956224
6264
6393
6404
6538
6564
6607
6676
6750
6774

製品名Server
DaemonServerServerDaemonServerServerServerServerServerDaemonServerServer6825

Server6832
6930

ServerParser10290

Parser

10709
10720
10768
10777

ServerParserDaemonServer10877

Server

10893
10912

ServerServer10938

Server11037

Server11038

Server

11056
11071
11077
11079
11098
11114
11119
11158
11161
11172
11175
11181
11208

ServerServerServerServerServerServerServerServerServerServerParserServerServer

内容
Put back ppm as tolerance unit for fragments
New Daemon installer.
Need introductory page / tutorial
Search form should accept URL of data file as URL argument
Sort out all Unicode issues in Daemon
Add NA/AA to the stats file
Several scripts still using mod_file and substitutions
Increase max length of database name
Display normalisation factors used in quantitation in export
Web browser form should get progress info and link to report asynchronously
Vista UAC/virtualisation issues need addressing
Want a separate file for 'own' modifications
If fail to open searches.log for writing, retry
ms-monitor.exe performance; also using a surprising amount of CPU when it
should be relatively idle
Changing priority doesn't change it on the cluster nodes
ET match with 'same' score as non ET match is not discarded.
Add classes to facilitate communication with a remote Mascot server via
HTTP
Suppress No taxonomy indexes warning unless applied to all databases
if charge is 9+ or more, "pep_exp_z" value is -100
Request to add support for AB SCIEX MS Data Converter
Configurable CSV and XML export should have no-duplicate peptides option
On the cluster node, compressed files need to be in a sequence directory
structure as on master
Add summary table of modifications found in search
Improved behaviour for chimeric spectra
Non-memory mapped database cycles between "Trying to unmap files" and "Inuse"
Allow FASTA file upload in Database Manager
login.pl does not return a correct response for web authentication in thepresence of domain qualified user names
Performance issue in cluster mode
Autorefresh selected pages in Database Manager
Add overview table of update schedules in Database Manager
Database Manager: autodetect proxy settings on Windows
Support IE 10, IE 11, latest Firefox and latest Chrome
Predefined database definitions need descriptions
Report count of queries with matches above threshold
Dead end in DB Manager if the downloaded file is not a FASTA file
Allow use of HTTP proxy server for FTP in Database Manager
Enable support for file:// URLs in Database Manager
Make access to XML files more thread safe
Report Builder: filter on number of unique significant sequences
Search crashes with no error message for a mod with 20 sites in 1 group最初にお読みください（Mascot Server version 2.5 (2.5.1) Windows 版）

11213
11217
11223
11226
11227
11232
11234
11235
11236
11241
11254
11263

ServerServer
ServerServerServerServerParserParser
ParserServerParserServer11268

Server

11276
11277
11279
11280

ServerServerServerServer11299

Server

11302
11330
11331
11334
11355
11358

ServerServerServerServerServerParser11361

Daemon

11362
11367
11372
11373
11374
11381
11386
11392

ServerServerServerServerDaemonServerServerParser11393

Server11399

Parser

11400
11403
11404
11407

ServerServerServerServer11409

Parser11411

Parser11413

Server

11416
11420
11422

ServerServerParser5

Pitiful little file crashes percolator.exe
Database Manager shouldn't write mascot.dat in place
Percentage progress should be based on number of bytes transferred
Checkbox to disable family grouping
Add pI and coverage as columns
FTP wildcards are shown in DB Manager but are not editable
Move quantitation subroutines to Parser
New method ms_mascotresults::getProteinEmPAI()
Improve ms_shapiro_wilk documentation
Enhance spectrum graphics with Spectrum Viewer
Add new method for number of instances of a given modification
Big Mascot search from Daemon with security enabled gives Error M00454
Report p-values for quantitation ratios, not just whether significantly
different from 1
Verify that peptide charges > 9+ and < 9- workHighlighting in fragment table incorrect for some sequence tags
Export percolator p-value and q-value
Add mzTab export format
Allow multiple choice when matching predefined definitions to custom
definitions
Delete a database from database manager and confusion occurs.
Review mascot init script for LinuxUse Parser to calculate emPAI
Need to flush upper I/O layers before releasing file lockhttpd.conf Access control keywords change in Apache 2.4
Combining resfiles: check that quantitation methods match
Get error when task database in MS SQL Server and open external processes
dialogProtein View fills logs with 'Use of uninitialized value' error
Result file compression / decompression must preserve mtime
No way to change database type (NA/AA) in DB Manager
Unformatted sequence string for NA database doesn't work
Daemon could warn when you edit a parameter set with invalid mod
Update example ET search
Search crashes using new Pepsin
Need to be able to return std::string & parameters in Java
Display more information in Peptide View for MS/MS spectra with nofragments
Simplify and reduce requirements for specify location of the unimod andquantitation schema files when using ms_mascotresfile
Target FDR code failing to reach target
Setting search priority on Linux fails to do anything
Protein Family Summary has slowed down since 2.3
Report Builder column editing buttons are confusing
Temporary cdb file created even when MSPEPSUM_DISCARD_RELOADABLE notspecified
Save qmatch and qploghole in the cdb file to improve performance
Invalid taxonomy name class (type material |) in
file ../taxonomy/names.dmp
Should be able to ask for target FDR in export script
Cluster mode crashes if number of variable mods greater than 9Under Windows, file sizes stored in cdb files are limited to 32 bits

最初にお読みください（Mascot Server version 2.5 (2.5.1) Windows 版）

11424
11425
11427
11434
11435
11437

ServerParserServerServer
ServerServer11438

Parser

11442
11443
11444
11448
11449

ServerServerDaemonServerServer

11454

Parser11456

Parser11458

Server

11460
11461
11463

ServerServer
Server11467

Parser

11470
11471
11473
11477
11478
11483
11485
11486
11488
11494

ServerServerServerServerServerParserServerParserServerServer

11495

Parser

11496
11497
11498
11499
11500
11505
11510
11513

ParserServerServer
ParserServerServerServer
Parser11517

Server11518
11527
11531
11538
11539
11540
11545

ServerServer
ServerParserParserServerParser

6

Allow normalising to selected sequences or accessions in Mascot reports
Faster function to get ions score for any query and rank
Add "silent" progress mode so that IIS doesn't kill disconnected search
Put systems in place to generate HTML files for shipper from wordpress
Ensure we can ship a new Percolator executable
mzML file takes 3 hours to 'unpack' and 1 minute to search
getObservedCharge() needs an optional parameter for specifying the summaryor decoy summary section
IT_MODS at query level cause segfault
Setting MaxQueries to 100 million causes all searches to use a lot of memory
Rewrite Daemon as .NET application
Javascript needs updating
Add login info to HTML header
Add a function to return the address and port of the default proxy server(Windows only)
Mascot security loophole when using command-line session
Duplicate matches when quant method has exclusive mods and constrain searchis truemscreatepip.exe crashes with IPTL test dataset
Tidy up one-letter codenph-mascot.exe should accept URL of data file as URL argument
Add a new MSPEPSUM flag to specify using homology threshold for ignore ionsscore below
Export original and modified NA sequence in ET searches
Dendrogram tiny in Chrome 26
Peptide view (and protein view) don't obey the ResfileCache directive
Get a slew of uninitialized value errors when exporting reporter quantCannot view report builder tab in decoy report
Add new flag for number of unique distinct sequences
Problems when FASTA URL contains ampersands in Perl 5.10.1 and older
Support Perl 5.16 and Perl 5.18
Search engine doesn't allow more than 16 components in label free
Database Manager should continue a download disconnected by proxy server
ms_mascotresults::findPeptides() returns peptides with status
DUPE_DuplicateSameQuery
Add isDataCached() for querying about cache file contents
Peptide view missing information for query with no match
Division by zero error in DB Manager if remote FASTA file is zero length
Cache numbers of hits above threshold for non-decoy searches
Database Manager: more robustness against corrupt configuration files
It's very hard to add a SwissProt type database without a reference file
DBManager fails to keep filename pattern while synchronising
Need to cache the protein coverage values
Creating new user and choosing multiple groups can have unpredictable
results
Userid spoofing doesn't work from Distiller
Endless loop after session timeout
Dendrograms have gone out of alignment in Chrome 28
Provide access to and use the new query_mods string where available
Update run_search.exe to work with new query-level mods strings
Report script support for new query-level mods string
Cron and ExecAfterSearch in mascot.dat cannot cope with spaces in paths

最初にお読みください（Mascot Server version 2.5 (2.5.1) Windows 版）

11547

Parser

11566
11582
11583
11584
11622
11631
11634
11644

ServerParserServerDaemonParserParserParserParser11646

Server

11680
11685
11686
11687
11696
11699
11700
11705
11708
11709
11711

ServerParserParserServerServer
ParserServerParserParserServerServer11712

Server

11713
11714
11715
11716

ServerParserParserServer11717

Parser11718

Parser11723

Server11726

Server

11736
11740
11744
11746
11755
11756
11760
11761

ServerServer
ServerServerServerServerServer
Server11765

Server11768

Server11770

Server11772

Server7ms_peptidesummary::getProtein() fails to return null when dbIdx isincorrect
Return job details in XML format from ms-status.exe
Session handle leak when checking for proxy settings under Windows
Update browscap.ini
Daemon complains about Mascot version when real problem is lack of licence
Rules on residue masses in mod_file make no sense
Sign the msparser.jar file using a CA trusted certificate
Report standard error as well as standard deviation
Switch from Xerces 2.3 to Xerces 3.1.1
Memory locking restricted to 32 bits, so 4Gb file limit. Severe memory leakfor files > 4Gb
Additional argument to keep connection alive by leaking bytes
New values for options section of mascot.dat
Global and per-group modification visibility for ms_umod_configfile
Update Perl scripts to enforce per-group modification visibility
Option to create brief results for Daemon
Add support for file:// and ftp:// to ms_http_helper class
Don't show target FDR buttons when Percolator is used
Improved behaviour for chimeric spectra
ms_peptide::getAnyMatch() is broken in 2.4.4
Database Manager does not check for SECTASK_ACCESSDBSETUP
Add TargetFDR and Unigene sections to output for Daemon auto-export
Error tolerant search is displaying possible modifications that areoutside tolerance when #13C=1 or 2
Could show the quantitation component for all precursor methods
Improved functionality for proxy use with ms_connection_settings
updateForInstaller() changes for Mascot 2.5
Need proxy settings editor in db_gui.pl
If peptide ratios are manually excluded from a protein ratio then values
from duplicate same query are used
Add functions to retrieve tree of distinct peptides
Pop-up for possible error tolerant mod assignments should not show excluded
mods
Changes in reporter ion quantitation normalisation settings not carriedthrough to protein_view
Configuration Editor. Linux build. Cannot add new modification.
Allow long database names
Acquire task ID automatically in batch mode
Merged results with no hits gives "No result file name supplied"
Support Perl 5.16 (Windows and Linux) and Perl 5.18 (Linux)
Faulty HTML encoding when redirecting
HTTP Error 404.3 when trying to download .opt files
Guest cannot edit users or groups in security_admin.pl(fatal) HEAD request succeeded for
ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz, but GET did not; cannotcontinue
Searching for peptide with variable mod fails if it's a non-significant
match unique to a subset
Increase the maximum URL length and query string length for IIS
Database Manager should retry after FTP timeout when using HTTP proxy forFTP最初にお読みください（Mascot Server version 2.5 (2.5.1) Windows 版）

11774
11779
11785
11792

ServerServer
ServerServer

11794

Server11795

Server11797

Parser11800

Server11804

Server8Show MS data URL instead of MS data file in reports
pip format changed in Percolator 2.06
New argument to ms-geterror.exe for displaying detailed help of an error
mi_pop_handler.pl not handling missing insight_percolated.log silently
A single Mascot search for two databases is counted as 2 searches on thedatabase status page and erroneously prevents new searches run if max limit
is reached.
When setting up NCBI nr, "Can't find the session file requested"
ms_datfile::updateForInstaller shouldn't update parse rules if DatabaseManager is being used
If ms-monitor fails to run test search there is no error in errorlog onLinuxUpdate htdig configuration with new exclude_urls

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