最初にお読みください（Mascot Server version 2.6 (2.6.0) Windows 版）

1

最初にお読みください
Mascot Server version 2.6 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」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_v2.6_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。

バージョンアップ前のバージョン(バージョン2.5 及びそれ以前)からバージョン2.6 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_v2.6_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. 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2.6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2.6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
1. スペクトル・ライブラリ検索
スペクトル・ライブラリ検索機能を実装し、既存の配列データベース検索環境に統合しました。検索エンジンはNIST MSPepSearchを利用しています。

2. スペクトル・ライブラリ作成
お客様が実行したMascot検索の検索結果ファイルからお客様独自のスペクトル・ライブラ
リを構築することができます。

3. その他
・MS2スペクトルにマッチしたペプチド（Peptide Sequence Match：PSM）の数に加えて、異なるアミノ酸配列（Sequence）の数に対するFDR計算をサポート
・デフォルトの検索結果表示を有意なPSMだけを使った内容に変更
・Mascot Daemon：コマンドラインによるMascot検索をサポート
・その他（ http://www.matrixscience.com/ help/november2016.html ）バージョン 2.5 からの変更点
4 頁 に バ ー ジ ョ ン 2.5.0 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_6.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 2.6 (2.6.0) 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がMascot Server version 2.6に対応していない場合は、スペクトル・ライブラリのリストは表示されず、FASTAデータベースのリストだけが表示されます。
(2) 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、WebサーバがIISであればそのまま動作すると思ますが、Apacheを使っている場合は動作しません。Mascot Server version 2.6では「Private」コピーとしてのPerlを内蔵していますので、スクリプトのshebangラインを#!/usr/local/mascot/perl64/bin/perlに変更してください。

最初にお読みください（Mascot Server version 2.6 (2.6.0) Windows 版）--------------------------------------------------------

Windows OS の各バージョンに対応する注意点-------------------------------------------------------(1) 32ビット版のWindows、Windows XP、Windows Server 2003はサポートしていません。

3

最初にお読みください（Mascot Server version 2.6 (2.6.0) Windows 版）

4------------------------------------------

バージョン 2.5.0 からの変更点-----------------------------------------次の表ならびに http://www.matrixscience.com/mascot_support_v2_6.html をご覧ください。

ID
4487
4504
5484
5926
6572
6780
6925
10717
10763
11014
11032
11147
11169
11178
11249
11261
11273
11324
11379
11429
11436
11466
11481
11534
11636
11638
11639
11662

Component
DaemonDaemonServerDaemonDaemonServerServerDaemonParserServerServerServerServerDaemonDaemonDaemonServerServerServerServerServerServerParserParserParserServerServerDaemon

11667
11690
11697
11725
11732
11773
11778
11782
11801
11816
11823
11829
11830
11859
11893
11897
11918
11935
11939

ParserDaemonParserParserParserParserServerServerServerServerServerParserServerServerServerServerServerServerServerDescription
Daemon needs status line
Columns in status tab are all string sort
Add options for which columns to display in ms-review.exe
Need filters for status tab
Daemon could show search %complete and add a kill button?
Should include data file name in the search log
Residue at protein N-term modifications broken
Add "Waiting for completing previous task" to [Schedule] in Task Editor
Replace PLPA library with hwloc
Site analysis could be reported even when only one match
Report mass delta relative to corrected mass for 13C matches
Using a predefined definition for, say, NCBI_NA_template makes no sense
Integrate spectral library search
Mascot security passwords recorded in plain text in the webserver search log
Too many searches being run at once causes search title to recurse
Daemon enters infinite loop when shutdown by the restart manager
ms-getseq POST request fails if there is a space in an accession.
Yellow 'popup' in family summary not wide enough
M00047 The process cannot access the file because it is being used by another process.
The installer could add an exception to the Windows firewall to allow port 80 accessExport script caching speedup for huge files when calling from command line
TargetFDRPercentages is missing from not.mascot.dat
Target FDR 1% gives 1.32% and failure, even though 0.91% is possible
Description for decoy protein always says random sequence
Improve Makefile on Linux
Database Manager User interface changes
Show a URL in addition to command-line parameters when showing export_dat_2.pl arguments
Use the -batch command line for nph-mascot to avoid IIS cancelling search if Daemon is stopped.
Use client.pl?last_error to get error messages without a %s
Output more progress reports when grouping proteins
Could create a result node for every file so as to persist any error message
Infinite loop in ms_mascotresfile::readLine()
Support public and internal API help documentation for ms_parser.
Mascot Server reporting a ratio calculated from two negative numbers
Where is query 14 in example iTRAQ search
Don't recreate Percolator pip file unless really needed
Search form fails to handle multiple databases in manual error tolerant search
Tidy up format controls for results with quantitation
Error message encoding is incorrect
Confusing command line help describing arguments for ms-createpip.exe
ProteinsInResultsFile setting 2 test should be greater than or equal
Roll-up of changes to Manual, release notes, and HTML pages for 2.6
Fatal error generating dendogram
RESID links need new URL
Not an ARRAY reference at ../bin/modules/DBManager/Workhorse/DatFileTools.pm
Want Mascot Security users and groups sorted alphabetically in Daemon etc.
Bare bones search form doesn't include data file URL
Config editor rejectes legal comp qualifier in quantitation method

最初にお読みください（Mascot Server version 2.6 (2.6.0) Windows 版）

11953
11966
11985
11986
11988
11991
11992
11994
12001
12003
12007
12018
12022
12026

ServerServerServerServerServerServerServerServerServerServerServerParserParserParser

12032
12036
12037
12039
12043
12045

DaemonParserParserServerDaemonServer

12046
12047
12053
12059

ServerDaemonParserServer

12060
12062
12065
12066
12068
12069
12070
12085
12096
12099
12101
12104
12106
12108
12109
12116
12121
12123
12125
12128
12129
12134
12136
12137
12141
12151
12154
12156

ServerServerServerParserServerServerServerServerServerServerParserServerParserServerDaemonDaemonParserServerServerDaemonServerServerServerServerServerDaemonServerServerShould be possible to upload licence file to Mascot ServerSpectrum Viewer colours should be configurable in mascot.dat
Google / Chrome translate causes search submission to failSetting SplitNumberOfQueries to 100 or 10 can crash mascot.
Unimod and masses sections in results files are confusing for BZX and UOJCGI executables and scripts fail to reference favicon.ico in HTML head
Export of metabolic quantitation search results incorrect
Highlight matches to Mr(calc) rounded to given number of decimal places
Command line args for export should not include a session ID
The formver=1 search form is broken for PMF
Replace the ions score cut-off edit box with a checkbox
No reliable way to reject one hit wonders in quantitation
GCC warnings in Parser, which may or may not be relevant
When results file has hundreds of thousands of protein hits, caching has gaps between progressmessages
Cannot submit searches to IIS when NTLM authentication enabled
Need to be able to search for individual ET mods
New colour settings in mascot.dat for Spectrum Viewer
custom XML fails to validate
Roll-up of feature requests for Daemon 2.6 taken from testing 2.5.1 Twiki pages
When patching 2.5, the mascot\config\unimod\usermod.xml file gets overwritten by the default
one
Remove usermod.xml and daemon_2_5_0_setup.exe from the shipper image
Roll-up of errors to be fixed in Daemon 2.6 taken from testing 2.5.1 Twiki pages
Need example for protein family grouping
Distiller memory efficient multi-file project broken if server 2.5.x running in cluster mode andsearch has more queries than SplitNumberOfQueries
Percolator problems
Database configuration details appear to hang if FASTA file is huge and not really a FASTA file
Export of large result file takes forever
ms_databases should inherit from ms_customproperty
MS Data File path gets lost on repeat search
Clean up usermod.xml when creating new unimod.xml
Merge changes to elements and mod_bricks from usermod.xml into unimod.xml
In Report builder filtering a report on a modification (acetylation) hangs in a loop
Incorrect message: Parse rule produces duplicate accessions
Reports slow for EST databases with thousands of sameset proteins
Support C# in Mascot Parser (using SWIG)
Ensure new Javascript files are sent to the browser after Mascot update
Test harness: format the exponent of doubles identically on both Linux and Windows
Elapsed time displayed incorrectly
Merge DTA fails if line endings not DOS
UNC filename corruption
Mascot security doesn't allow multiple Fasta files to be specified in multiple groups
offer choice of PSMs or distinct peptide sequences for FDR calculation
Auto decoy not working for NA database
Auto export fails for Mascot DAT File and MGF Peak List
Don't autorefresh when uploading FASTA file in Database Manager
mzIdentML export of retention time broken
Shapiro-Wilk never succeeds for a very large sample
Enable AA + NA searches
Protein mass is not nominal
Add link to open containing directory for cached files
Split by query cluster mode fails if data per node > 2Gb
Never see combinations of certain mods5

最初にお読みください（Mascot Server version 2.6 (2.6.0) Windows 版）

12158

Server

12161
12162
12165
12168
12170
12171
12172
12173
12174
12175
12176
12177
12178
12179
12180
12181
12182
12183
12184
12188
12191
12208
12212
12216
12220
12222
12227
12230
12232
12236
12237
12239
12241
12244
12260
12264
12265
12266
12269
12272
12281
12282
12286
12288
12291
12293
12307
12310
12311
12317
12318
12321
12334

DaemonServerParserServerServerParserParserParserParserServerServerServerServerServerServerServerServerServerServerServerServerServerParserDaemonServerParserDaemonServerParserServerServerDaemonServerParserDaemonServerParserServerServerServerParserServerServerServerParserServerServerServerServerParserParserServerServer6

Crash in nph-cache_families.pl if search has multiplex peptide match with a variable mod that has no
0 Da neutral loss
Export defaults should be taken from mascot.dat
Add a re-compress link
iTRAQ broken if ITOLU=ppm
Large peptide ratio values are not being formatted correctly in master_results_2.pl
Integrate spectral library searches
Read library matches from new library_summary and library_matches sections
Do protein inference with both database and library matches
Changes to mascot.dat for spectral libraries
New mascot.dat Options for library search and compression tool configuration
Estimate library match significance from library score distribution
Map library sequences to protein accessions at the end of the search
Parse and convert NIST library search results into Mascot or internal format
Search a spectral library in parallel with the main database searchCompress spectral libraries
Allow creating, editing and deleting spectral library definitions
Allow searching multiple AA and NA databases and spectral libraries
Display a combined database and library search report
Display library and observed spectra for a library match
Display library protein hits correctly
New tool for importing search results into a spectral librarymzML file that causes a crash on public web site
Write a perl script that deletes old cache files and compresses .dat files
index error in ms_mascotoptions::isDefaultTargetFDRPercentage
Completed search details added repeatedly to MySQL TaskDB after connection problem
Default column width for priority for ms-review.exe is 2, but needs to be 4
Access to new HTTP classes from Perl is not possible and documentation needs improving.
Uninstall and reinstall gives message: "ABSciexMSDC not available"
IPC logs displayed in search progress page
Top scoring peptide matches missing from some queries in merged results
Fixes to mzIdentML 1.1 compliance
Crash on Mascot Server with small error tolerant search in cluster mode and specificities per group
Mods are being split on an internal comma within a mod name
GetSeq and GetTaxonomy too slow
Occasional failure to write session files for IP address and computer name
Changes to support MDRO 2.5.1 (or 2.6.0)
Can't locate object method "!isMissing" when sorting p-value column in Report Builder
Parser class ms_http_helper needs to support https
Procedure to create results cache files needs to delete *.flg filemods duplicated in result file if fixed and variable have overlapping specificities
SVG graphic fails to appear due to parenthesis in mod nameJava interface improvements
clarify statement on MS MS Results Interpretation help page
Crash on public website with error tolerant search (Probably only Linux)
Display library status in ms-status.exe
Add a common logging interface to msparser
Handle database definitions of type MSP in matrixlib
Need to look at ET search speed optimisation
GI sequence identifiers are being phased out at NCBI
In batch mode, mascot.dat options for security rights for creating daily directory are ignored
ET search scores and mod counts look wrong
Support reading, parsing and indexing of NIST msp files
When did you last see a grey block?
Misc. Installer changes for Server 2.6

最初にお読みください（Mascot Server version 2.6 (2.6.0) Windows 版）

12335
12336
12347
12349
12351

DaemonServerDaemonParserServer

12354
12355
12357
12364
12366
12367
12369

ParserServerServerParserDaemonParserDaemon

12370
12374
12375

ServerParserDaemon

12380
12381
12384
12385
12388
12390
12391
12395
12404
12405
12408
12414
12415
12416
12419
12422
12427
12428
12430
12431
12433
12434
12438
12444
12448
12449
12451
12456
12458
12460
12463
12468

ServerDaemonServerServerDaemonDaemonParserParserServerParserParserParserServerServerServerServerServerParserParserParserParserServerParserServerParserParserServerParserParserParserServerParser

12469
12476
12477

ServerDaemonServer12480

Server7

Changes to support spectral library search
ms-gettaxonomy.exe overflow
It is possible to clear the taxonomy combo box in the parameter editor
Extend Percolator calculations to all ranks
Can't call method "should_do" on unblessed referenceat ../bin/modules/DBManager/WWW/Database.pm line 1625.
ms_ms1quantitation can't handle quantified unassigned peptide matches
Protein View: "cannot find None in mascot.dat" when UniGene=None
Installer needs to disable Timer_MinBytesPerSecond test in IIS
Error tolerant search reports junk matches and average threshold score of 0
Need way to specify output path for generic import filter
Parser test differences since build server started
Button to copy parameter name and path from Parameter Editor to "Parameter set" field in Task
Editor tab
Mascot test differences since build server started
Add peak list data file name in search log
Request visual indicator on task editor tab that shows whether auto export or external process
options are set.
mascot.dat changes when clicking Choose accession parse rule
Daemon could bypass web server for large files when running on the Mascot Server
Database Manager cannot stat FASTA file if it is actually a dead symbolic link
Disallow creating a database whose name differs from an existing one only by case
Distiller registration is broken on 64-bit systems
Add export and import for TaskDB
Add ms_mascotresults_params object and new constructors to use it
Need method to merge ms1 quantitation data in ms_ms1quantitation
Use VS2012 for building Mascot Server (was 2005). Also use Perl Parser modules built with VS2012
mzIdentML export of fragment matches fails if ITOL is ppm
Add XML_SCHEMA_DIRECTORY option to ms_mascotresfile getXMLschemaFilePath
Support Python 3
decoy_type should be printed per database instead of per search
Display mixed AA and NA searches correctly
db_manager.log doesn't roll over correctly when it reaches maximum size
Inconsistent decoy results when searching 2 databases with different number of threads
If ms-monitor.exe can't create mascot.control, it core dumps
Create Python scripts for the Parser Documentation
Score distribution does not include ET matches and the values look wrong
Support Visual Studio 2015
http_client must work on Linux
When unimod files access is denied, no error is displayed
Supply Perl, Python and Java modules built using VS2012 rather VS2005/VS2008
matrix lib function getFileLength on Windows reports zero length file when it is being written to
Cache file with missing quantitation if errors due to missing xsd file
Classes that inherit from ms_errors with a copy constructor don't copy the base ms_errors object
Change http://xxx/mascot/x-cgi/ms-status.exe?Show=REGPRODUCTKEY to be clearer
Add new bool parameter to the ms_masses ms_umod_configfile constructor
Inconsistent handling of whitespace in user parameters between cache and non-cache mode
Set: WARN_NO_PARAMDOC = YES in msparser.doxy
Under Windows, calls to _findfirst, _findnext, _findclose use wrong parameter type
Add isSamesAs(...) comparison method to ms_umod_modification class and encapsulated dependantclassesSpectral library changes for 3rd party API
Enable quant xml export
Existence check for retention times in reports and ms-createpip.exe needs to consider all
rtinseconds values
Support Percolator 3.0

最初にお読みください（Mascot Server version 2.6 (2.6.0) Windows 版）

12481
12488
12497
12498
12500
12501
12507
12508
12509
12512
12516
12518
12519
12520

DaemonServerParserParserServerServerServerParserServerServerServerServerServerServer

12521
12528
12532
12536

ServerServerServerServer

12540
12560
12562
12564
12566
12571
12576
12577
12578
12582
12583

ServerParserServerServerServerParserServerServerParserServerServer

12584
12588

ServerServer

12594
12596
12597

ServerServerServer

12601
12602
12604

ServerServerParser8

Should have different user agent strings for GUI and engine
NCBI web site is dropping HTTP in September 2016
New overloaded method ms_inputquery::getRetentionTimes() for reading all rtinseconds values
Duplicate should be selected by expectation values
Rename "weighted" protein ratio to "summed intensities"
Ownership and permissions of current directory are not inherited correctly from mascot/sequencemzIdentML1.1.0.xsd missing from shippers
mascot.dat setting for ions score cutoff checkbox / edit box
Peptide containing residue with zero mass gets zero ions score
Don't allow double quotes in accessions when choosing parse rules
Corrupt session file causes ms-monitor.exe general protection fault
Database Manager reports too many false positives for synchronisation
Do not print undefined Protocol Reporter values in Quantitation method configuration
Configuration Editor must read data from usermod in priority and J, O and U should always beeditable
Don't allow double quotes in accessions when compressing databaseShow detailed task log in reverse chronological orderDon't try to autoscroll to the most recently expanded or collapsed page fragment
When changing database type between AA and NA, use the new recompress facility of
ms-status.exe instead of trying to delete the .stats file
Add a simple recompression interface to ms-status.exe
Error saved in a cache file is repeatedMulti-cpu build issues [Don't include in release notes]
Change default Protein Ratio Type from 'weighted' to 'average' in reporter quantitation methods
nph-mascot crashes when using a database which requires newer taxonomy than the installed one
Need SDK 80 release of Parser for the Mascot Installer. [Don't add to release notes]
Default Windows httpd.conf changes
Changes to Linux 2.6 installer
Changes to updateForInstaller() for Mascot Server / Parser 2.6
Read config/db_manager/postinstall.conf and add or enable missing databases
Failure to remove updated URL parameters after using the finder toolbar causes, in some cases, aredirect loop
"Bad Request" under IIS when giving an invalid value as _sigthreshold in Protein Family Summary
Disabling a database and changing it's parse rule numbers at the same time causes ms-monitor.exe
to barf
Need a new ms-status.exe command for returning the path to the .msp or .fasta filenph-mascot.exe hangs at the end of pmf search
When synchronising or importint a database definition with a UniGene index, fatal error when trying
to warn that the UniGene index doesn't exist
Protein View causes warning "Negative taxID -1 is not valid for ms-gettaxonomy.exe"
Score histogram is empty when the score list is all -1's
ms_inputquery::fillPeakList() fails to parse a peak list if it contains no colons

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。

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