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1. Mascot Security administration 3 Mascot Security Administration Utility Microsoft Internet Explorer Gle Edt View Favortes Tools Help GO Bak O x a A A Seach Favores Address http t41 dee mascot x cgi security _admin pl Mascot Security Administration Logged in as Administrator Users Groups Add Add admin Administrators daemon Delete PowerUsers Delete system Daemons Edit MascotintegraSystem Edit Options Option Value Option Value Security enabled F Verify IP address Vv Session timeout 21600 Logging level Boo Default password expiry 365 spo ra server http integra 8080 topaz on passord s Mascot Integra database integra Use session cookies Lj Integra Oracle server integra Stst SOSC S Save options This is the URL of a local Mascot Integra server Will generally be on port 8080 Default http integra 8080 topaz 2 javascript void 0 MASCOT Administration amp Configuration 2007 2012 matrix Science ets All security configuration is browser based The top level page of the security administration utility looks like this There is a list of users a list of groups and a few options If you hold the mouse over any of the blue text help will appear at the bottom of the screen The options shown on this page are global options which apply to all users Reference You can t disable security from here it has to be done on the server2. t41 dmcieascotfegimaster rests pofter data 200S0531 FO0413S dat MATRIX BETE SCIENCE SEH MHF Log Fie monoa s Sence Mascot Search Results GET r Jobs PID dbase User Name Version 2 1 0 Licensed to Matrix Science Demor Search title Submitted from Immunology 20050531 by Mascot Daemon on T41 DNC e MS data file galah f_drive mascot_test_data LCQ ismunology LCQ Digest03 06 Mascot Security Database IPI_human human 2 32 41519 sequences 19421139 residues Timestamp ae ee oe ee EE Error ian is not permitted to submit searches of type MIS Username fian Password 2 Rights Reserved a eS 4 5 Probability Based Mouse Score Peptide Summary Report FOSAS I Poptde Sammoy a Help Significance threshold p lt o os Max number of hits 20 Standard scorning MudPIT sconng Ions score cut off f Show sub sets 7 Show pop ups Suppress pop ups Sort unassigned Decreasing Score Require bold red SelectAl _ SelectNone SearchSelected M Error tolerant _ AchiveRepon MASCOT Administration amp Configuration 2007 2012 matrix science Sonne A group member will be able to view the search log see their results but when they try to do a repeat search access is denied Example Daemon amp Distiller Z Mascot Security Administration Utility Microsoft Internet Explorer File Edt view Favorites Tools Help QOQ x A E Posen She Favorkes 2 i JGR Onn F S 2 hittp
3. 1 Current YES Cluster Nodes flim Lm O OK 80 free lem 100 free on 15 free 10 25112 Limx ox 81 free 100 free 19 free 10 25113 Limx ox 81 free 100 free 19 free 1025114 Limx ox 81 fee 100 free 19 free 1025115 Limx ox 82 free 100 free 23 free MASCOT x Administration amp Configuration 2007 2012 Matrix Science yes If you have a Mascot cluster it is almost as easy to administer as a single machine Everything is reported and controlled through the master node The Cluster Nodes table provides a an overview of the search nodes smiley faces or green unhappy faces If you need a closer look at one of the search nodes follow the links to view the search node log files 34 Sources of Information Using Mascot Server e The HTML help pages Mascot Server installation configuration and troubleshooting e Installation amp Setup Manual e Support pages on www matrixscience com Using Mascot Daemon e Online help F1 Using Mascot Distiller e Online help F1 Anything not answered by the above e support matrixscience com MASCOT Administration amp Configuration 2007 2012 Matrix Science Soc Finally a reminder of where you can find technical information about Mascot 35
4. User type Standard Mascot user x se enabled v ascot Integra user Computer name IP address Agent string i User authenticated using web server MASCOT Administration amp Configuration 2007 2012 Matrix Science T There are potential issues with older legacy applications that interface with Mascot but don t have code to support the security system Since session ids are saved as cookies and since most Windows applications that access web sites use Microsoft Internet Explorer libraries it may be sufficient just to login from an Internet Explorer browser window before starting the application Alternatively you can use one of the special user types 15 Example 3 party applications Computer name IP address e Never have to log in from that computer e Use the computer name IP address as the name Agent string e Can determine the agent string from the web server logs e Not secure because someone could create another app to use this agent string Web server authentication MASCOT Administration amp Configuration 2007 2012 Matrix Science ues These methods are less secure than a password protected login but ensure that all applications are able to connect somehow 16 Mascot Security general tips e Plan carefully before implementation e Login as admin to perform admin tasks e Enabling Mascot security doesn t stop your server from being hacked e Moving Mascot to another c
5. of interest to system administrators Setup amp Installation Manual ps Release Notes E MAS COT Administration amp C onfig uration 2007 2012 Matrix Science Soc The Mascot Installation amp Setup manual is linked from your local Mascot home page If you need detailed information on any aspect of Mascot installation or configuration this is the place to look Installation amp Setup http t61 jsc mascot pdf manual pdf Windows Internet Explorer JO hitp f61 fsc imascot pdt jmanusl pdf Fie Edt GoTo Favorites Help Wst of We R E hpiRrer simascotipd marnsal pd E deh o Page G Toos sB ee eleie k O R oHm K cobor Asn l d g ones A At first sight this may seem a strange mix of m z and Da The reason is that we need to avoid matches from 1 fragment ions whatever the charge on the precursor If the arguments are anything other than 1 1 a single notch is used where the first argument is the mass offset of the beginning of the notch and the second value is the mass offset of the end of the notch For the precursor in the last example if the arguments were 1 4 then the notch would run from m z 799 5 to m z 802 0 However if the precursor charge was 1 then the notch would be from m z 799 to m z 804 The mascot dat setting can be over ridden in a search by using the search parameter CUTOUT Note that the peaks removed by this filter are not recorded in the result file changing this parameter in a rep
6. t41 jscimascot x cgi securty_admin pl Mascot Security edit group Daemons Logged in as John Cottrell Unique ID 4 Users in Group Users not in group daemon Name Daemons admin johne pughl Tasks that cannot be SEARCH Allow no enzyme pmf searches performed by group members SEARCH Maximum number of concurrent searches per user SEARCH Maximum mascot search job priority Add task SEARCH Maximum number of queries per search SEARCH Maximum execution time v Tasks that can be Task Parameter eee by group C SEARCH Allow pmf searches To remove tasks selet C SEARCH Allow ms ms and SQ searches one or more check boxes and press Remove Remove C SEARCH Allow msms no enzyme searches C SEARCH Allow all fasta databases to be searched O VIEW See all search results with a USERID O VIEW See search results without USERID field C GENERAL View config files using ms status C CLIENT Mascot Daemon is allowed to submit searches C CLIENT Mascot Distiller is allowed to submit searches C CLIENT For Mascot Daemon allow spoofing of another user MASCOT Administration amp Configuration 2007 2012 matrix Science SCIENCE Client software like Mascot Distiller and Mascot Daemon requires special privileges The Mascot Daemon user must have the security token Mascot Daemon is allowed to submit searches The group settings shown here are appropriate for either a Daemon or Distiller client View config files
7. 0 078 Edit cl Chlorine 34 96885272 35 453 Edit Cu Copper 62 9295989 63 546 Edit e electron 0 000549 0 000549 Edit F Fluorine 18 99840322 18 9984032 Edit Fe Iron 55 9349393 55 845 Edit H Hydrogen 1 007825035 1 00794 Edit Hg Mercury 201 970617 200 59 Edit Iodine 126 904473 126 90447 Edit K Potassium 38 9637074 39 0983 Edit Li Lithium 7 016003 6 941 Edit Mo Molybdenum 97 9054073 95 94 Edit N Nitrogen 14 003074 14 0067 Edit Na Sodium 22 9897677 22 98977 Edit Ni Nickel 57 9353462 58 6934 Edit o Oxygen 15 99491463 15 9994 Edit pP Phosphorous 30 973762 30 973761 Edit s Sulfur 31 9720707 32 065 Edit Se Selenium 79 9165196 78 96 Edit Zn Zinc 63 9291448 65 409 Edit MASCOT Administration amp Configuration 2007 2012 matrix science ets You may need to add or edit an element or an amino acid but its fairly unlikely Configuration Editor Z Unimod Microsoft Internet Explorer Fle Edt View Favores Tools Help Q gt AG Osun fers O R Address 4 http www unimod orgimodifications _ist php goto 7 UNIMOD Unimod Logged as unimod Log out Change password Advanced search Add Search for Any field v Contains v ee et new how all Page 7 of 27 20 Select Unselect all Delete selected Accession PSI MS Name Interim name Description Monoisotopic Average Composition mass mass Label 13C 6 15N 4 13C6 15N4 13C 6 15N 4 Silac 10 008269 9 9296 C 6 13C 6 N label 4 15N 4 Ser gt Pro Ser gt Pro substitution 10 020735 10 03
8. 168 8 135 z5 1 1 5 Type of srch MIS Enzyme Yes CPU utilisation O Job requests No requests Kill Pause Resume Back to main status page a MASCOT Administration amp Configuration 2007 2012 Matrix Science T You can drill down from the database status page to a list of searches for each database and then down to the details of an individual search as shown here If necessary you can kill or pause a search from this page or change its priority 29 Log files search log viewer gt Mascot SearchLog Windows Internet Explorer coi ms review exe CalledFromForm 1 amp doofile 2Flogs 2F searches log start 1 amp howMany 50 Y p X Gt Yew Favortes Tools Mascot SearchLog MASCOT search lo Version 2 3 0 Licensed to Matri Science in house DELL5000 1 processor Log File logs seerchesiog Start at 1 end 1 start 1 how many 50 78036 in log 7085 after filters Data dir O O O O O v z D O B dbase User Name Email Ti In start time O i SwissPro Tue Mar 23 13 50 42 2010 11 s Tue Mar 23 13 49 55 2010 19 User read re SwissPro FA User read re SwissPro User read re IPI_huma olittle edu User read re IPI_huma u Mar User read re IPI_huma Thu Mar 11 11 00 53 2010 379 User read re SwissPro alizer doolittle edu Tue Mar 09 09 12 44 2010 16 User read re SwissPro Fn Mar 05 13 52 20 2010 1114 Userreadre NCBinr alzer doolittle edu Fn Mar 05 09 48 39 2010 642
9. 79 H 2 C 2 Of 1 Label 13C 9 1SN 1 13C9 15N1 13 9 1SN 1 Silac 10 027228 9 9273 C 9 13C 9 N label 1 1SN Thr gt Ile Thr gt Ile substitution 12 036386 12 0538 Thr gt Asn Thr gt Asn substitution 12 995249 12 9988 Methylamine MethylamineST Michael addition with 13 031634 13 0418 methylamine Pro gt pyro Glu Pyroglutamic proline oxidation to 13 979265 13 9835 pyroglutamic acd Trp gt Oxolactone oxolactone Tryptophan oxidation 13 979265 13 9835 to oxolactone Methy Methyl Methylation 14 015650 14 0266 8 g2 g 6s g2 o g s g3 o g o g ss Asp gt Glu substitution 14 015650 14 0266 MASCOT Administration amp Configuration 2007 2012 matrix Science T The modifications file unimod xml is an XML representation of a public database called Unimod This is the interface to the public database From time to time you should update your local file by downloading the latest file using the links in the Unimod help Configuration Editor 3 Mascot configuration Microsoft Internet Explorer File Edt View Favorites Took Help Q OX BD Pah fers O Z E http t41 isc mascot x cgi ms config exe u 1 183042968 Mascot Configuration Modifications Administrator Modifications Title Monoisotopic Average Composition Phe gt Ser 60 036386 60 0966 H 4 C 6 O Copy Delete Print Phe gt Tyr 15 994915 15 9994 O Copy Delete Print Phe gt Val 48 000000 48 0428 C 4 Copy Delete Print Phenylisocyanate 119 037114 11
10. 9 1207 H S C 7 NO Copy Delete Print Phenylisocyanate 2H S 124 068498 124 1515 2H S C 7 N O Copy Delete Print Phospho 79 966331 79 9799 H O 3 P Copy Delete Print Phosphoadenosine 329 052520 329 2059 H 12 C 10 N S O 6 P Copy Delete Print Phosphoguanosine 345 047435 345 2053 H 12 C 10 N S O 7 P Copy Delete Print PhosphoHex 242 019154 242 1205 H O 3 P Hex Copy Delete Prnt PhosphoHexNAc 283 045704 283 1724 H O 3 P HexNAc Copy Delete Print Phosphopantetheine 340 085794 340 3330 H 21 C 11 N 2 O 6 P S Copy Delete Print PhosphonibosyidephosphoCoA 881 146904 881 6335 42 C 26 N 7 0 19 P 3 S Copy Delete Print PhosphoUndine 306 025302 306 1660 H 11 C 9 N 2 O 8 P Copy Delete Print Phycocyanobilin 586 279135 586 6780 H 38 C 33 N 4 O 6 Copy Delete Print Phycoerythrobilin 588 294785 588 6939 H 40 C 33 N 4 O 6 Copy Delete Print Phytochromobilin 584 263485 584 6621 H 36 C 33 N 4 O 6 Copy Delete Print Piperidine 68 062600 68 1170 H 8 C S Copy Delete Print Pro gt Ala 26 015650 26 0373 H 2 C 2 Copy Delete Print Pro gt Arg 59 048347 59 0705 H S C N 3 Copy Delete Print Pro gt Gin 31 005814 31 0140 HNO Copy Delete Print Page 21 of 26 Goto page Ph to Pr v lt lt G gt page size 20_ Add new modification Main menu Help Window MASCOT Administration amp Configuration 2007 2012 Matrix Science SoC If you need to add a new modification that will be of interest to others it s best to add it to the p
11. Administration amp Configuration MATRIX SCIENCE Installation amp Setup Matrix Science Home Windows Internet Explorer E v htp Rt l jscjmascot file Edt yew Favorites Joos tip We Be Barre science Home CR db gt e Gta e dit settings e Current session information Whether or not Mascot security is enabled in order to comply with the licensing conditions access to this Mascot server must be restricted to authorised users We strongly recommend that your server is protected by a secure firewall For more information start from the WWW Security FAQ Mascot Utilities Your system administrator may have restricted access to these utilities Database Status View the status of all the sequence databases Links to database statistics search status log files etc Search Log A tabular view of the search log Can be filtered to find specific search results Configuration Editor Browser based configuration editors including security administration and sequence database management Mascot Daemon Mascot Daemon is a client application which automates the submission of data files to a Mascot server It runs under Microsoft Windows 2000 and later Install Upgrade Troubleshoot Mascot Documentation Help on using Mascot and understanding the resuMg is contained in these HTML pages Click on Help at the top of the page to browse the help topics or use the keyword search facility The followiNg documents are mainly
12. User read re SwissPro alizer doolittle edu Wed Mar 03 11 25 08 2010 22 User read re SwissPro alzer doolittle edu Tue Mar 02 18 57 27 2010 129 User read re SwissPro Tue Mar 02 16 00 26 2010 1112 User read re SwissPro Su Tur Mar 02 154527 2010 6 Lo Local intranet MASCOT Administration amp Configuration 2007 2012 matrix Science T This is the search log viewer You can sort on any of the columns using the radio buttons and then pressing Sort filter The checkboxes determine whether a column is shown or hidden The two hidden columns are Ti for title and In for intermediate file This is a hyperlink to display the raw mascot result file but you can only see the first two characters of the file name which are The hyperlink in the first column displays the formatted result report You can set the number of lines to display and whether to start at the beginning or end of the file You can also filter the display by entering text into the edit boxes For example your user name or a word from the search title If you have split the search log into sections then you can choose which file to display by entering the path 30 Log Files Troubleshooting Other useful files e Database compression lt database gt current lt database gt errors e Database taxonomy lt database gt current lt database gt NoTaxonomyMatch txt e Database statistics lt database gt current lt database gt stats e Web serv
13. d NO Number of threads 1 Current YES Name contaminants Faemil usr local mascot_2_4 0 64 sequence contaminants current contaminan Filename contaminants 20120206 fasta Pathname usr local mascot_2 4 0 64 sequence contaminants current con Status In use State Time Mon May 14 19 11 02 searches 0 Mem mapped YES Request to mem map YES Request unmap NO Mem locked NO Number of threads 1 Curren t YES EST mouse Family usr local mascot_2 4 0 64 sequence EST_mouse curren t EST_mouse_ EST_mouse_20120429 fasta Pathname usr local mascot_2_4 0 64 sequence EST_mouse curren t EST_mouse_ In use State Time Mon May 14 19 11 04 searches 0 Mem mapped YES Request to mem map YES Request unmap NO Mem locked NO Number of threads 1 Curren t YES Human EST Family usr local mascot_2_4_0 64 sequence Hwwan_EST curren t H _EST_ fe Human _EST_111 fasta Pathname usr local mascot_2 4 0 64 sequence Human_EST curren t Human_EST_111 In use Statistics Unidentified taxonomy State Time Mon May 14 19 11 06 searches 0 lt gt MASCOT Administration amp Configuration 2007 2012 matrix Science T The database status page has links to many of the log files mentioned earlier This is the starting point for troubleshooting problems especially those connected with database updates When Mascot Monitor first starts there is a single entry per database Once a database has been upda
14. ea is to rename the file periodically For example searches log 20060301 The system will then create a new one automatically If the search log is accidentally damaged a new one can be created by scanning all the result files on the disk If you move Mascot to a new machine yov ll probably want to transfer or rebuild searches log The other important file is mascot job which contains the next job number If you don t copy this across your job numbers will start all over and you ll have to sort the search log by descending start time to locate the most recent searches Some people import the search log into a database application so as to make it easier to search or filter especially if it gets very large 27 Log files database status Mascot search status page C fi bogong MASCOT search status page Version 2 4 0 Matrix Science in house test LCC7 X8BP QN77 7MT8 YQJH Licence Info Logged n as John Cottrell logout Using 5 nodes and 10 processors 0 searches running Search log monitor log error log Error message descriptions nodelist tst Do not auto refresh this page apple Family usr local mascot_2 4 0 64 sequence apple current apple fasta apple 20120411 fasta Pathname usr local mascot_2_4 0 64 sequence apple current apple_ 20120411 fas Status In use Statistics State Time Mon May 14 19 11 02 searches 0 Mem mapped YES Request to mem map YES Request unmap NO Mem locke
15. eat search Determines the number of protein title lines saved to each results file 1 Asin Mascot 1 7 and earlier only proteins that appear in the Summary section will appear in the Proteins section 2 Include proteins with at least one top ranking peptide match toa peptide of length greater than MinPepLengthInPepsummary 3 Include all proteins BE 7 Program Reference 3 8 1 0 File Formats d 9 Taxonomy 10 Mascot Daemon 3E 11 Cluster Mode MASCOT Administration amp Configuration 2007 2012 Matrix Science Soc This is an administrator s manual not a user manual You won t find much relating to how to submit a search or how to interpret the results User help is in the Mascot HTML pages Installation amp Setup eMascot Security eConfiguration Editor eLog Files Cluster mode MASCOT Administration amp C onfigur atiONn 2007 2012 Matrix Science Sei These are the topics we will cover in this presentation Mascot Security Examples of how Mascot security can be used e Ordinary users can browse configuration files and status screens but not make changes e Certain sequence databases are private to a group of users e Limit some users to one search at a time while others can run many searches simultaneously e Limit the length of searches from a particular group to 1 hour e Prevent certain users submitting no enzyme searches e Let customers view the results of search
16. ed Configuration and program files are distributed and updated automatically from the Master node e A cluster behaves and looks like a single server Need dedicated or partitioned hardware e Cannot allocate machines dynamically e General purpose server farm usually not cost effective MASCOT Administration amp Configuration 2007 2012 matrix Science ets In cluster mode every search is distributed to all the cluster nodes and each node searches a portion of the sequence database This means that you get the parallel processing advantage for a single spectrum Search results are returned to the master which merges them and writes the result file to disk All master node communication is via TCP IP This uses simple socket based communication A parallel operating system is not required Configuration and program files are distributed and updated automatically from the Master node so the cluster behaves and looks like a single server Sometimes we are asked about running Mascot on a general purpose server farm that is being used for other applications For standard PC hardware the cost of the Mascot licence is greater than that of the hardware For a given capacity the lowest cost route will always be a minimum number of licences on dedicated hardware If you want to run Mascot on machines that are part of a larger cluster best to partition off a number of nodes either for exclusive Mascot use or where Mascot has absolute prio
17. er access and error logs eSystem event or message log MASCOT Administration amp Configuration 2007 2012 matrix Science T The first three files are most easily viewed using the links in database status Sometimes there will be nothing in the Mascot logs because the problem is external to Mascot Sometimes it can be useful to look at the web server logs or even the operating system logs The Windows Event Viewer control panel administrative tools allows you to browse Windows system messages 31 Cluster mode External Intranet TCP IP lt TCP IP Mascot master TCP IP dodo TCP IP switch TCP IP Mascot node 2 Mascot Cluster Topology Mascot node 3 MASCOT Administration amp Configuration 2007 2012 matrix Science T Just a few words about Mascot cluster mode Mascot supports cluster operation using a Beowulf like topology Mascot supports cluster mode as standard whenever the licence is for 4 CPU s or more You just have to hook up an appropriate number of PC s on a local LAN 32 Cluster mode Every search is distributed to all the cluster nodes e Each node searches a portion of the sequence database e Get the parallel processing advantage for a single spectrum e Search results are returned to the master which merges them and writes the result file to disk All master node communication is via TCP IP e Simple socket based communication e No parallel operating system requir
18. es run for them without being able to submit searches themselves MASCOT Administration amp Configuration 2007 2012 matrix Science T Mascot security is not a substitute for a firewall It won t stop your server being hacked or infected by a virus It is a way of managing and allocating the Mascot Server resources Mascot Security enable disable Z Matrix Science Mascot Security Microsoft Internet Explorer loj x Elle Edit yew Favorites Tools Help a GQ Bak O a L Leah SeFavortes O O a wW OD Address a http t41 dmc mascot cgiflogin pl Go MA TRIX SCIENCES HOME MASCOT iHELP Go Mascot Security Mascot Security Mascot Security is not enabled Copyright 2005 Matrix Science Ltd All Rights Reserved c Command Prompt _ 5 x C Inetpub MASCOT bin Denable_security pl The password for the admin account has been set to admin but you will be required to change it at the next login C Inet pub MASCOT bin gt _ MASCOT Administration amp Configuration 2007 2012 matrix Science et When Mascot is first installed Mascot security is disabled So if you try to log in you will see this message To enable security open a command prompt or a shell on the Mascot server and change to the mascot bin directory Type enable_security pl This takes a few seconds If you forget the administrator password it can always be reset to admin by running this script again
19. he Mascot Setup and Installation manual To drop an option clear the value field No changes are written to mascot dat until you choose APPLY SaveLastQueryAsc SaveEveryLastQueryAsc LastQueryAscFile logs lastquery asc InterFileBasePath usr flocal mascot_2_4_0_64 data InterFileRelPath data ResultsPeriScript _ cgi master_results pl ResultsPeriScript_2 _ cgi master_results_2 pl ResultsFullURL http bogong mascot_2_4_0_64 cgi master_r ResultsFullURL_2 http bogong mascot_2_4_0_64 cgi master_r NoResultsScript _ cgi master_results p TestDirectory data test MascotCmdLine _ cgi nph mascot exe MascotControlFile data mascot control MascotNodeControlFile data mascotnode control MascotJobIdFile data mascot job MASCOT Administration amp Configuration 2007 2012 matrix Science T The Configuration Options section deals with various global settings stored in mascot dat Remember that in Mascot 2 4 all the sections of mascot dat that deal with sequence database configuration may be re written at any time by Database Manager If you ve been in the habit of editing mascot dat in a text editor only the Options and Cluster sections can be modified safely unless you decide never to use Database Manager There are two configuration files that are missing from the configuration editor Taxonomy categories taxonomy and Cluster geometry nodelist txt If you need to make changes to these you still have to use a
20. he config directory The syntax for each of these files 1s described in the manual 18 Configuration Editor Mascot configuration e C fi Obogong Mascot Configuration John Cottrell Elements Element masses Amino Acids Amino Acid Data Modifications Modification definitions Symbols Symbols used in chemical formulae Enzymes Enzyme definitions Instruments Fragmentation Rules Quanttation Quantitation Methods Configuration Options Global Options in mascot dat Database Manager Sequence databases Parse Rules and automated downloads Security Security Administration Pages MAS COT Administration amp C onfig uration 2007 2012 Matrix Science Sec You can edit these files in a text editor but it is easier and safer to use the browser based Configuration Editor The first 4 entries are interfaces to different sections of unimod xml Configuration Editor F Mascot configuration Microsoft Internet Explorer Fle Edt View Favortes Tools Help Q x aA Q Osun ferv O 2 Address 2 itp 041 jsc mascot x colms config exe u 1 1SSO429688ELEMENTS_SHO W 1 Elements Element Name Monoisotopic Da Average Da 13C Carbon13 13 00335483 13 00335483 Edit 15N Nitrogen1S 15 00010897 15 00010897 Edit 180 Oxygenis 17 9991603 17 9991603 Edit 2H Deuterium 2 014101779 2 014101779 Edit Ag Silver 106 905092 107 8682 Edit Au Gold 196 966543 196 96655 Edit Br Bromine 78 9183361 79 904 Edit C Carbon 12 12 0107 Edit Ca Calcium 39 9625906 4
21. iguration Editor F Mascot configuration Microsoft Internet Explorer Fle Edt View Favortes Tools Help Ox O ix AOD Osun feres Address http t41 Jscfmascot x colfms config exe u 11830429688ENZYMES_SHOW 1 Mascot Configuration Enzymes Administrator Title Sense Cleave at Restrict Independent Semispecific Trypsin C Term KR P no no Edit Delete Arg C C Term R P no no Edit Delete Asp N N Term 6D no no Edit Delete Asp N_ambic N Term DE no no Edit Delete Chymotrypsin C Term FLWY no no Edit Delete CNBr C Term no no Edit Delete C Term C Term N Term C Term Lys C C Term Lys C P C Term Pepsina C Term Tryp CNBr C Term CNBr Trypsin no no Edit Delete Formic_acd no no Edit Delete no no Edit Delete no no Edit Delete no no Edit Delete no no Edit Delete no no Edit Delete no no Edit Delete no no Edit Delete no Edit Delete Trypsin P C Term V8 DE C Term V8 E C Term semiTrypsin C Term N Term C Term M M KR 8 0 K K FL KMR TrypChymo C Term FKLRWY no no Edit Delete KR BOEZ Ez KR 8D K LysC AspN no no Edit Delete None MASCOT Administration amp Configuration 2007 2012 Matrix Science yes Similarly for Enzymes and Instruments The other sections Quantitation Database Manager and Security have been touched on in earlier presentations Configuration Editor C fi Obogong Configuration Editor Edit Mascot Options Detailed descriptions of individual options can be found in Chapter 6 of t
22. is required because both clients need to retrieve configuration information from the server like a list of the databases that are available Mascot users can be given the privilege to submit searches under other user names This is particularly useful in a core lab when customers only have privileges to see their own search results so the instrument operator needs to submit their searches under individual customer log in names The security task is For Mascot Daemon allow spoofing of another user 13 Example Daemon amp Distiller Mascot Daemon Untitled New Run Data import filter btiix Science Masc Noe y Schedule Start now Start at fi s snuary 2006 C Real time monitor C Follow up Search priority fo 7 Actions Auto print results External processes Follow up No follow up required booo ja j resu Date oiro adime ra fal fo a Merge MS MS files into single search R Passdatsto None H MASCOT Administration amp Configuration 2007 2012 Matrix Science aa If this has been enabled for the user who is running Mascot Daemon then a drop down list of other Mascot user names will be enabled on the Task Editor tab 14 Example 3 party applications Older applications that submit searches to Mascot won t have their own login Try logging in using Internet Explorer before running the application cookies Use one of the special user types
23. n Enter their full name and email address The user will be able to change this I ll return to the choice of user types later most users should just be standard Mascot users MATRIX SCIENCE Make sure that the account is enabled and then select one or more groups for the user to belong to 10 Example Core Lab Customer If you don t want the customers to be able to do any searches but just view the results then just give them the access to tasks SEARCH Allow all fasta databases to be searched VIEW See search results from other people in your own group VIEW Allow user to view the search log ADMIN Allow use of Database Status application MASCOT Administration amp Configuration 2007 2012 Matrix Science T In a core lab you may want a group that enables customers to view their results In this case only give them rights to perform these tasks You must allow all fasta databases to be searched otherwise they won t be able to view reports However they can t perform PMF or MS MS searches because this task is missing i Example Core Lab Customer Oek O A gO South ira O Ov eM OS a Ble Edt yew Favortes Tools Help Ay Adtres E herp R41 dmcjmascotj cgims review exeCalea E DO x Qe O x a A seh T Favores O Oe a MASCOT search log Osk O i 2 Dlh roes O O a M O A3 address E hetp Ra1 dmejmascotjcgiogn pireferer hetp sanzt nzm EJ Go Adddress 48 http
24. omputer Just copy over user xml group xml and security_options xml MASCOT Administration amp Configuration 2007 2012 matrix Science yeti I can t stress enough that you should plan what you intend to do before you start Think carefully about what groups you want to create As any Unix administrator will tell you it s always best to separate your administration and user tasks However we can t force you but that is why the default admin user cannot submit searches It is very important to understand that Mascot security does not provide protection against a malicious hacker Hackers don t attack a server through Mascot they ve probably never heard of Mascot They attack through weaknesses in the operating system and through flaws in well known applications like the web server It is still essential to have a dedicated firewall between the Mascot server and the Internet 17 Configuration Editor Almost everything in Mascot is configured using text files in the config directory e General settings mascot dat e Masses and modifications unimod xml eEnzymes enzymes e MS MS ions series fragmentation_rules e Taxonomy categories taxonomy eCluster geometry nodelist txt eSecurity group xml user xml security_options xml security_tasks xml MASCOT Administration amp Configuration 2007 2012 Matrix Science Sei Almost everything in Mascot is configured using these text files in t
25. rch log eCan search specific databases eCan view other peoples results MASCOT Administration amp Configuration 2007 2012 matrix Science T There are 30 different tasks that members of a group can be allowed to perform for example Mascot Security add user 2 Mascot Security Administration Utility Microsoft Internet Explorer File Edit yew Favorites Tools Help x 2 Search Se Favorites Omk 0 Address http t41 dmejmascot x cgifsecurity_admin pl E oo Go Logged in as Administrator Mascot Security Administration Add user Name Password Password expiry Full name Email address User type Account enabled C Never C Default Force change at next login Dohn Smith ismith someuni edu 0 003 User is a member of the following groups MascotintegraSystem Standard Mascot user 7 Multiple selections can be made by means of the shift and control keys platform dependent F Add user y Cancel A user must belong to one or more groups If a user belongs to multiple groups then they have rights to perform the any of the tasks specified for any of the groups l javascript void 0 ff ff d Local intranet MASCOT Administration amp Configuration 2007 2012 matrix Science Adding a new user is very simple The Administrator must enter a username and password and it is usually a good idea to force the user to enter a new password when they first logi
26. rity over other processes Mascot cluster nodes cannot be dynamic because of the size of the database files The time taken to move these files between machines or even just in and out of memory would always be unacceptable 33 Cluster mode Mascot search status page wit NCHINI ramliy usr 1ocalsmascot_ lt 4 U_ b4 sequence NUbinr current NUbing rasta NCBInr_ 20120710 fasta Pathname usr local mascot 2 4 0 64 sequence WCBInx current MCBInz 20120710 Statistics Compression warnings Unidentified taxonomy State Time Ved Jul 11 15 14 44 searches 0 Mem mapped YES Request to mem map YES Request unmap NO Mem locked NO Number of threads 1 Current YES Name rice protreome Famil e usr local mascot_2_4_0_64 sequence rice proteome current rice prote Filename rice proteome 20120613 fasta Pathname usr local mascot_2 4 0 64 sequence rice proteome current ri Status In use State Time Wed Jul 11 15 14 18 searches 0 Mem mapped YES Request to mem map YES Request unmap NO Mem locked NO Number of threads 1 Current YES Name ITAG2 3 Family a usr local mascot_ 2 40 _64 sequence ITAG2 3 current ITAG2 3_ fasta Filename ITAG2 3_proteins fasta Pathname usr local mascot_ 2 KE 0_64 sequen e ITAG2 3 current ITAG2 3_protei Status In use State Time Ved Jul 11 17 20 13 searches 0 Mem mapped YES Request to mem map YES Request unmap NO Mem locked NO Number of threads
27. ted there are two entries one for the old file and one for the new We need this double view because of the way databases can be updated in the background without interrupting searches During database exchange while the new file is compressed and tested searches can still be submitted to run against the old file Once the new file is ready all new searches are run against the new file So on a busy server there may be a period when you have searches running against both the old and new files As soon as the last search on the old file has completed the old database can be taken out of use Mascot monitor takes care of all of this automatically 28 Log files database status F Mascot search status page Microsoft Internet Explorer Fie Edit View Favorites Tools Help Q Ox BQH On ms FY oneni Mt 4 Address http kosla mascot x cgi ms status exe Autorefresh true Show JOBDETAILS Database 1 Which v Ed co Mascot Job status Job 2696 Database NCBInr Job Number 2696 Process ID 2996 Task ID User Name Cat R Pillar User ID s 0 User email leaf mul ch Search title A few peptides from an LCMS run Percent complete 2 Intermed file data 20060201 F002696 dat Start time Wed Feb 01 11 20 57 2006 End time Searching time 0 Upload time 0 Query prep time 0 Whole process time 0 Job status Searching Priority current value 0 Change this by IP address 192
28. text editor You can find full details of the file formats in the manual 25 Log Files Troubleshooting The files in the logs directory are the first place to look if there is a problem e installation install log Windows only e General errors errorlog txt e Database update utility ftp_log txt e Mascot Monitor events monitor log eSecurity events security log e Cluster bootstrapping load_node log Unix only e Cluster communication ipc log MASCOT Administration amp Configuration 2007 2012 Matrix Science Sei The log files are the first place to look if there is a problem Most of these files can be accessed from a browser via links in the database status utility which we ll come to ina minute 26 Log files searches log e May need to split roll over the log if it gets very large e Can be recreated using ms makesearchlog exe e If you move Mascot to a new machine transfer searches log and mascot job along with the search results files e Tab separated values easily transferred to spreadsheet or relational database MASCOT Administration amp Configuration 2007 2012 matrix Science ets Every Mascot search adds a new line to the searches log If the server is busy the log files can get very large For most of the logs you ll probably want to delete the file from time to time The searches log is different and you ll probably want to keep all entries indefinitely Best id
29. ublic Unimod database so that the information is available to all Mascot users Also if you add a definition to your local file it will be lost if you download an updated file from the public server On the other hand there may be reasons why you have to create a local definition such as confidentiality or because you are just experimenting If so use the Modifications section of the configuration editor Configuration Editor F Mascot configuration Microsoft Internet Explorer File Edt View Favores Tools Heb Q D x a e JO seach Sie Fevortes 2 Address http t41 iscimascot x coiims config exe u 1183042968 Edit Modification Piperidine Administrator Name Title Piperidine Fullname Piperidination Delta Delta Monoisotopic 68 062600 Average 68 1170 H 8 C S Symbols 13C vil The chemical composition of the modification as a delta between the modified and unmodified residue or Aj terminus For example if the modification removes an H and adds a CH3 group the Composition would be shown as H 2 C The formula is displayed and entered as atoms optionally followed by a number in parentheses The number may be negative and if there is no number 1 is assumed Hence H 2 C is the same as H 2 C 1 MASCOT Administration amp Configuration 2007 2012 Matrix Science aa The user interface is fairly self explanatory and help is displayed for each field when you mouse over the label Conf
30. using the disable security command The session timeout is in seconds After this period of inactivity the user will be required to login again The password expiry time is in days After this period of time the user will be required to enter a new password Set to 0 to allow passwords to be permanent Any new password must be at least this length Session cookies are automatically destroyed when the browser is closed With some browsers session cookies are not shared when a new instance of the browser is opened which might mean that a user has to login again for each new window opened If verify the IP address is set then any request to perform a privileged action will compare the IP address that the request is coming from with the one originally used to login Logging level should normally be left at 3 Mascot Security role based Users Groups e Login name e Name e Password password e List of members expiry e List of allowed tasks e Full name email address e Account enabled disabled e Member of one or more groups MASCOT Administration amp Configuration 2007 2012 matrix Science T Mascot security is role based This means that privileges known as tasks are assigned to groups not individual users Users gain these privileges by being members of one or more groups Mascot Security tasks For example e Allow PMF search e Allow MS MS search e Maximum number of queries eCan view the sea
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