Administration & Configuration
Contents
1. 15 9994 Edit 30 973761 Edit 32 065 Edit 78 96 Edit 65 409 Edit New element Main menu a Local intranet MATRIX SCIENCE MASCOT Administration amp Configuration 2007 2010 matrix science You may need to add or edit an element or an amino acid but its fairly unlikely Configuration Editor A Unimod Microsoft Internet Explorer File Edit View Favorites Tools Help Q sxx Q ix E p Search she Favorites e3 amp i Powermarks Wu A Address amp http fwww unimad org modifications list php goto 7 U N IMOD protein modifications for mass spectrometry Help Unimod Logged as unimod Log out Change password Advanced search Records Per 531 Page Page 7 of 27 20 wj Add Search for Any field v Contains v Details found new Accession PSI MS Name 267 Label 13C 6 15N 4 652 269 Label 13C 9 15N 1 664 Methylamine Pro gt pyro Glu Trp gt Oxolactone Methyl Select Unselect all Delete selected Interim name 13C6 15N4 Ser Pro 13C9 15N1 Thr gt Ile Thr gt Asn MethylamineST Pyroglutamic oxolactone Methyl Asp Glu Description 13C 6 15N 4 Silac label Ser gt Pro substitution 13C 9 15N 1 Silac label Thr gt Ile substitution Thr gt 4sn substitution Michael addition with methylamine proline oxidation to pyroglutamic acid Tryptophan oxidation to oxolactone Methylation A2. e Not secure because someone could create another app to use this agent string Web server authentication MASCOT Administration amp Configuration 2007 2010 matrix science MATRIX These methods are less secure than a password protected login but ensure that all applications are able to connect somehow 18 Mascot Security general tips Plan carefully before implementation Login as admin to perform admin tasks Enabling Mascot security doesn t stop your server from being hacked Moving Mascot to another computer J ust copy over user xml group xml and security options xml MASCOT Administration amp Configuration 2007 2010 matrix science ae 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 19 Configurat
3. to add it to the public Unimod database so that the information 1s 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 24 Configuration Editor i Mascot configuration Microsoft Internet Explorer File Edit View Favorites Tools Help Qs o ix 2 Search She Favorites e Powermarks If 9 Address E http t41 jsc mascot x cgi ms config exe u 1 183042968 Edit Modification Piperidine Administrator Name Title Piperidine Fullname Piperidination Delta Specificity Ignore Masses Misc References Monoisotopic 68 062600 Average 68 1170 congo H 8 C 5 Symbols 13C w 1 The chemical composition of the modification as a delta between the modified and unmodified residue or 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 v javascript void 0 CP Local intranet MASCOT Administration amp Configuration 2007 2010 matrix Science PATIN The user int
4. 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 2010 matrix science eae Mascot security 1s role based This means that privileges are assigned to groups not individual users Users gain these privileges by being members of one or more groups Mascot Security tasks For example Allow PMF search e Allow MS MS search e Maximum number of queries e Can view the search log e Can search specific databases e Can view other peoples results MASCOT Administration amp Configuration 2007 2010 matrix science eae There are 30 different tasks that members of a group can be allowed to perform for example Mascot Security add user E Mascot Security Administration Utility Microsoft Internet Explorer E File Edit view Favorites Tools Help Back x iz JP Search sy Favorites A O7 s J 9 3 Address e http t41 dmc mascot x cgi security admin pl j Go Mascot Security Administration Add user Logged in as Administrator User is a member of the following groups Name Password C Never Password C Default MascotIntegraSystem expiry Force change at next login Full name Dohn Smith Email address fismith someuni edu User type Standard Mascot user 7 Multiple selections can be made by means of t
5. 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 so cannot be recovered by changing this parameter in a repeat search ProteinFamilySwitch see NoResultsScript Determines the number of protein title lines saved to each results file 1 AsinMascot 1 7 and earher 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 to a peptide of length greater than MinPepLengthinPepsummary 3 Include all proteins Unknown Zone MASCOT Administration amp Configuration 2007 2010 matrix science MATRIX SCIENCE 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 Mascot Security Configuration Editor Log Files Cluster mode MASCOT Administration a
6. 0 Logging level Default password expiry 568 vc Integra server http integra S0BQ topaz Coe p 5 Mascot Integra database integra Use session cookies Integra Oracle server ntegra iti CCt Save options Help window Use this configuration application to add delete edit users and groups For further help on any input parameter hold the mouse over the blue text 3 Local intranet MASCOT Administration amp Configuration 2007 2010 matrix science MATRIX The user has been added successfully To edit a group we select it and choose Edit Mascot Security add user E Mascot Security Administration Utility Microsoft Internet Explorer File Edit View Favorites Tools Help Q Bak iX iz Search e Favorites O7 Address amp http t41 dme mascot x cqi security_admin pl Mascot Security edit group Guests Logged in as Administrator Logout Unique ID 1 Users in Group Users not in group Name Guests Tasks that cannot be SEARCH Allow ms ms and SQ searches performed by group members SEARCH Allow msms no enzyme searches SEARCH Allow no enzyme pmf searches Add task SEARCH Maximum mascot search job priority SEARCH Maximum number of queries per search Tasks that can be performed by Task roup members dad gt SEARCH Allow pmf searches To remove tasks solon ohe or mre D SEARCH Maximum number of conc
7. 1 329 052520 345 047435 242 019154 283 045704 340 085794 881 146904 306 025302 586 279135 588 294785 584 263485 68 062600 26 015650 39 048347 31 005814 Average 60 0966 15 9994 48 0428 119 1207 124 1515 79 9799 329 2059 345 2053 242 1205 283 1724 340 3330 881 6335 306 1660 586 6780 588 6939 584 6621 58 1170 26 0373 59 0705 31 0140 Administrator Modifications Title Monoisotopic Composition H 4 C 6 O Copy O Copy C 4 Copy H 5 C 7 N O Copy 2H 5 C 7 N O Copy H O 3 P Copy H 12 C 10 N 5 O 6 P Copy H 12 C 10 N 5 O 7 P Copy H O 3 P Hex Copy H O 3 P HexNAc Copy H 21 C 11 N 2 O 6 P S Copy H 42 C 26 N 7 O 19 P 3 5 Copy H 11 C 8 N 2 O 8 P Copy H 38 C 33 N 4 O 6 Copy H 40 C 33 N 4 O 6 Copy H 36 C 33 N 4 O 6 Copy H 8 C 5 Copy H 2 C 2 Copy H 5 C N 3 Copy HNO Copy Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Delete Print Page 210f26 Gotopage PhtoPr wj ssJe Pagesie 20 v Add new modification Help Window amp j Local intranet rf MATRIX SCIENCE MASCOT Administration amp Configuration 2007 2010 matrix Science Unimod is becoming fairly comprehensive If you need to add a new modification it s best
8. ASCOT Administration amp Configuration 2007 2010 matrix science MATRIX SCIENCE The first 4 entries are interfaces to different sections of unimod xml Configuration Editor i Mascot configuration Microsoft Internet Explorer DAR File Edit View Favorites Tools Help Qs Q ix E DO search She Favorites amp 2 d e B i Powermarks Wu 76 Address amp http jt41 jsc mascot x cgilms config exe u 1183042968 amp ELEMENTS SHOW 1 Elements Element 4 Name Monoisotopic Da Average Da 13C Carbon13 13 00335483 13 00335483 Edit 15N Nitrogenis 15 00010897 15 00010897 Edit 180 Oxygeni8 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 40 078 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 I 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 P Phosphorous S Sulfur Se Selenium Zn Zinc 15 99491463 30 973762 31 9720707 79 9165196 63 9291448
9. Administration amp Configuration MATRIX SCIENCE Installation amp Setup Matrix Science Home Windows Internet Explorer Gc P hd e http Jt 1 jsc mascot J X Pe File Edit View Favorites Tools Help Snagit d Matrix Science Home ta aem Page ic Tools e e Edit settings e Current session information F 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 resu is contained in these HTML pages Click on Help at the top of the page to browse the help topics or u
10. Anna Lizer alizer doolittle edu SwissPro Anna Lizer alizer doolittle edu SwissPro Anna Lizer alizer 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 Tue Mar 02 154527 2010 6 3 Local intranet User read re i SwissPro Pe T Tue Mar 23 13 50 42 2010 11 ROTG Pe Tue Mar 23 13 49 55 2010 19 User read re SwissPro C User read re SwissPro x User read re u Mar p e pes wo co User read re Thu Mar 11 11 00 53 2010 379 User read re Tue Mar 09 09 12 44 2010 16 User read re Fri Mar 05 13 52 20 2010 1114 User read re Fri Mar 05 09 48 39 2010 642 User read re Wed Mar 03 11 25 08 2010 22 User read re ak na wo peat wo uA e O A pak ea wo UJ iaa e pa wo lisi e ak wo eo e co wo m ay zo 20 MASCOT Administration amp Configuration 2007 2010 matrix science eae 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 dis
11. IN Allow use of Database Status application MATRIX MASCOT Administration amp Configuration 2007 2010 matrix Science CENCE 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 13 Example Core Lab Customer E Mascot SearchLog Microsoft Internet Explorer ls x Ele Edt View Favorites Tools Help 7 Z Matrix Science Mascot Security Microsoft Internet Explorer ii Oj x O O 3 iz 3 seh Araotes C gt M DO Ele Edit view Favorites Tools Help A aire cgi ms revi s Peptide S R t Submitted fi I k 20050531 by Mascot Daemon on T41 DMC Microsoft T a 1 i Address http ft41 dmc mascot x cqi ms review exe CalledF Peptide Summary Report Submitted from Immunology y Ma Q Back B x iz A D Search lt gt Favorites coy z File Edit view Favorites Tools Help MASCOT search log Qe O mM ad Prsearch 2 Favortes Og Les Address e http jt41 dme mascot caiflogin pl referer http 3a 2F 2 v Go Address amp http t41 dmce mascot cqi master_results pl file data 20050531 F004135 dat Version 2 1 0 Licensed to Matrix Science Demot MATRIX HOME MASCOT HELP Search Go Mascot Security Logged in as i
12. T bin gt _ MASCOT Administration amp Configuration 2007 2010 matrix science SRAT When Mascot is first installed Mascot security is disabled So if you try and login 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 Mascot Security administration E Mascot Security Administration Utility Microsoft Internet Explorer File Edit View Favorites Tools Help Back x iz JP Search e Favorites Address PES http t41 dme mascot x cqi 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 I Verify IP address Iv Session timeout 1600 Logging level n Default password expiry 38688 duced EC Integra server h amp 5 integra 8080 topaz pU password 5 Mascot Integra database negra Use session cookies r Integra Oracle server ntegra t lt CisCits Save options This is the URL of a local Mascot Integra server Will generally be on port 8080 Default http integra 8080 topaz H am
13. amp Configuration 2007 2010 matrix Science AMATRUX 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 DAR File Edit view Favorites Tools Help a Q e C2 ix a 5 yi Search Sie Favorites e LJ rel X G Snagit e Powermarks Hh A 9 Address e http t41 jsc mascot x cgi security_admin pl lt p co Mascot Security edit group Daemons Unique ID 4 Name Daemons Tasks that cannot be performed by group members Tasks that can be performed by group members To remove tasks select one or more check boxes and press Remove Logged in as John Cottrell Users in Group Users not in group SEARCH Allow no enzyme pmf searches SEARCH Maximum number of concurrent searches per user SEARCH Maximum mascot search job priority SEARCH Maximum number of queries per search SEARCH Maximum execution time Task Parameter SEARCH Allow pmf searches SEARCH Allow ms ms and SQ searches SEARCH Allow msms no enzyme searches SEARCH Allow all fasta databases to be searched VIEW See all search results with a USERID VIEW See search results without USERID field GENERAL View config files using ms status CLIENT Mascot Daemon is allowed to submit searches CLIENT Mascot Distiller is a
14. an Edit Logout MATRIX y SCIENCE Sonir Log Fie Toge searcheslog s sczenc Mascot Search Results GETs Job PID dbase User Name oer ten Tron Drogy Email ian someuni edu e Oo o e Search title Submitted from Immunology 20050531 by Mascot Daemon on T41 DMC F F F A MS data file Agalah f_drive mascot_test_data LCQ immunology LCQ Digest03 06 Mascot Security Database IPI human human 2 32 41519 sequences 19421139 residues Timestamp 31 May 2005 at 14 50 16 GMT Error ian is not permitted to submit searches of type MIS 4135 2888 IPI human Ian from Immun 2928 IPI human Ian from Immun WV Usemame fian 1844 IPI human Jan from Immun NS 3260 IPI human Tan from Immun Password 3320 IPI human Ian from Immun 7 2072 IPI human Ian from Immun 3132 IPI human Ian from Immun aL f M 30 40 50 Copyright 2005 Matrix Science Ltd All Rights Reserved a Number of Hits T T Probability Based Mowse Score amp Done Local intranet A Peptide Summary Report Format As Peptide Summary 7 Help Significance threshold p lt 0 05 Max number of hits eo Standard scoring MudPIT scoring Ions score cut off 0 Show sub sets Show pop ups Suppress pop ups C Sort unassigned Decreasing Score 7 Require bold red Select All Select None Error tolerant Archive Report xi amp Done figi I Ini m Local intranet 7 MASCOT Administration
15. de IP Address OS Responding Physical Memory Swap file Disk space slave01 192 168 70 1 Linux OK 51 free 99 free 54 free slave02 192 168 70 2 Linux OK 44 free 99 free 53 free slave03 192 168 70 3 Linux OK 44 free 99 free 54 free slave04 192 168 70 4 Linux OK 45 free 99 free 53 free slave05 192 168 70 5 Linux OK 46 free 99 free 53 free slave06 192 168 70 6 Linux OK 41 free 99 free 53 free slave07 192 168 70 7 Linux OK 79 free 100 free 53 free slave08 192 168 70 8 Linux OK 79 free amp 100 free 53 free slave09 192 168 70 9 Linux OK 79 free 100 free 54 free slave 10 192 168 70 10 Linux OK 79 free 100 free 53 free slave11 192 168 70 11 Linux OK 79 free 100 free 53 free slave12 192 168 70 12 Linux OK 79 free 100 free 53 free slave 13 192 168 70 13 Linux OK 79 free 100 free 53 free slave 14 192 168 70 14 Linux OK 80 free 100 free 53 free Internet MASCOT Administration amp Configuration 2007 2010 matrix science ae 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 This is a good slide to finish on rows of happy smiling faces just like yours
16. eptides from an LCMS run Percent complete 2 Intermed file data 20060201 F002696 dat Start time Wed Feb O1 11 20 57 2006 End time i Searching time 0O Upload time t 0 Query prep time 0 Whole process time 0 Job status Searching Priority current value 0 Change this by 5 1 1 5 IP address 192 168 8 135 Type of srch MIS Enzyme Yes CPU utilisation 0 Job requests No requests Kill Pause Resume Back to main status page amp amp J Local intranet MASCOT Administration amp Configuration 2007 2010 matrix science Amar 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 30 Log files search log viewer Mascot SearchLog Windows Internet Explorer e Mascot SearchLog MASCOT search lo Version 2 3 0 Licensed to Matra Science in house DELL5000 1 processor Log File logs searches log Start at 1 end lstart how many 50 78036 in log 7085 after filters Data dir GETs O Job PID dbase User Name i Ti In start time Dur Oo Oo O O O O O v vi v m m Sc IL r1 UJ an ec N eo N feat wo Mo IPI huma oolittle edu IPI huma IPI huma SwissPro Anna Lizer alizer doolittle edu SwissPro NCBInr
17. erface is fairly self explanatory and help is displayed for each field when you mouse over the label 25 Configuration Editor E Mascot configuration Microsoft Internet Explorer DEAR File Edit View Favorites Tools Help Q sxx x x a I i 3 K M Powermarks ie 4 9 Address a http jt41 jsc mascot x cgilms config exe u 1183042968 amp ENZYMES SHOW 1 Mascot Configuration Enzymes Administrator Enzymes 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 BD no no Edit Delete Asp N ambic N Term DE no no Edit Delete Chymotrypsin C Term no no Edit Delete CNBr C Term no no Edit Delete C Term CNBr Trypsin C Term Edit Delete Formic acid cal Edit Delete C Term Lys C C Term Edit Delete Lys C P C Term Edit Delete Pepsin amp C Term Edit Delete Tryp CNBr C Term Edit Delete TrypChymo C Term Edit Delete C Term Edit Delete C Term Edit Delete C Term Edit Delete semiTrypsin C Term Edit Delete N Term LysC AspN Edit Delete i p C Term None L addnew enzyme J Mainmenu MASCOT Administration amp Configuration 2007 2010 matrix science ae Similarly for enzymes and instruments The other sections quantitation sequence database maintenance and security configuration have been touched on in earlier presentations There are two configuration files that are missing from the configuration ed
18. ervals of 1 ds Merge MS MS files into single search Jv Passdatato None MATRIX MASCOT Administration amp Configuration 2007 2010 matrix science SCIENCE 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 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 User type Standard Mascot user x Account aliis ups user enabled i IMS MASCOT Administration amp Configuration 2007 2010 matrix science MATRIX 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 17 Example 3 party applications Computer name IP address e Never have to log in from that computer Use the computer name IP address as the name Agent string e Can determine the agent string from the web server logs
19. ge Name MSDB Family C INETPUB MASCOT sequence MSDB t MSDB fasta Filename MSDB 20050227 fasta Pathname C edie added Use uence MSDB t MSDB 20050227 fasta Status In Statisti Compression warnings Unidentified taxonom State Time We d E 18 09 53 10 searche Mem mapped YES Request to mem dps YES Request unmap NO Mem locked NO Number of threads 4 Curren t YES NCBInr Family C INETPUB MASCOT sequence NCBInr curren t NCBInr fasta e NCBInr 20051029 fasta Pathname ipii inani equence NCBInr current NCBInr 20051029 fasta In use gy sti Compression warnings Unidentified taxonomy ime Wed Jan 18 09 53 13 s es YES Request to inea Mapa gods TES Mem locked NO reads 2 Curren t YES EST human Family C INETPUB MASCOT sequence EST_human curren t EST_human_ fa e EST_human_20021023 fasta Pathname C INETPUB MASCOT sequence EST human current EST human 20021023 fasta Not in use Statisti ime Thu Jan 19 23 15 43 searches 0 ed NO Request to SEM ERE ES pec uman N Mem locked NO f threads 2 C t NO Family C i INETPUB MASCOT sequence EST human curren t EST human fa e EST human 20060119 fasta Pathname C algo pidan ida equence e EST human current EST human 20060119 fasta In use statisti Unidentified taxonom MASCOT Administration amp Configuration 2007 2010 matrix science Amar The database status page has links to many of the log files men
20. he shift and control keys platform dependent Account Ie enabled Add user 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 javascript void o Edd amp J Local intranet MATRIX SCIENCE MASCOT Administration amp Configuration 2007 2010 matrix science When you add a user the Administrator must enter a username and password It is usually a good idea to force the user to enter a new password when they first login 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 Make sure that the account 1s enabled and then select one or more groups for the user to belong to 10 Mascot Security add user J Mascot Security Administration Utility Microsoft Internet Explorer 7 File Edit view Favorites Tools Help ay Q Back O x a 0 22 Search Se Favorites 42 iyo J 9 3 Address El http sfe4i dmejmascotjx coisecurty admmpl Go Mascot Security Administration Logged in as Administrator Logout User johns added successfully Groups Add Administrators PowerUsers Delete Daemons MascotIntegraSystem Options Option Option Security enabled Iv Verify IP address Session timeout 3160
21. ion 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 Enzymes enzymes e MS MS ions series fragmentation rules e Taxonomy categories taxonomy e Cluster geometry nodelist txt e Security group xml user xml security options xml security tasks xml MATRIX MASCOT Administration amp Configuration 2007 2010 matrix Science CENCE Almost everything in Mascot is configured using these text files in the config directory The syntax for each of these files 1s described in the manual You can edit these files in a text editor but it 1s easier and safer to use the browser based Configuration Editor 20 Configuration Editor E Mascot configuration Microsoft Internet Explorer i Ele Edit View Favorites Tools Help O x 5 O search Favorit i D Powermarks Bi Ap 9 Q a P m TQ p7 Searc avorites CS de Powermarl v Address e http Jt41 jsc mascot x cailms config exe Mascot Configuration Administrator Elements Element masses Amino Acids Amino Acid Data Modifications Modification definitions Symbols Symbols used in chemical formulae Enzymes Enzyme definitions Instruments Fragmentation Rules Quantitation Quantitation Methods Database Maintenance Sequence databases Parse Rules and Options Security Security Administration Pages amp J Local intranet M
22. itor Taxonomy categories taxonomy and Cluster geometry nodelist txt If you need to make changes to these you still have to use a text editor You can find full details of the file formats in the manual Log files The files in the logs directory are the first place to look if there is a problem e Installation install log Windows only General errors errorlog txt e Database update utility ftp log txt e Mascot Monitor events monitor log e Searches searches log e Security events security log e Cluster bootstrapping load node log Unix only e Cluster communication ipc log MASCOT Administration amp Configuration 2007 2010 matrix science MATRIX The log files are the first place to look if there 1s a problem Most of these files can be accessed from a browser via links in the database status utility which we ll come to in a minute Zi Log files searches log May need to split roll over the log if it gets very large Can be recreated using ms makesearchlog exe If you move Mascot to a new machine transfer searches log and mascot job along with the search results files Tab separated values easily transferred to spreadsheet or relational database MASCOT Administration amp Configuration 2007 2010 matrix science ae 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 t
23. llowed to submit searches CLIENT For Mascot Daemon allow spoofing of another user Save changes Cancel MASCOT Administration amp Configuration 2007 2010 matrix 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 chient View config files 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 s 15 Example Daemon amp Distiller Zt Mascot Daemon File Edit Help Task Editor Untitled New Run Data import filter EE z os 1 Scheduls Start now C Statat 15 08 23 426 January 2006 C Realtime monitor C Follow up Search priority o Actions Auto print results External processes Follow up No follow up required o Discard results Delete Add Files Repeat at int
24. mp Configuration 2007 2010 matrix science MATRIX These are the topics we will touch on in this presentation Mascot Security Examples of how Mascot security can be used Ordinary users can browse configuration files and status screens but not make changes 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 Limit the length of searches from a particular group to 1 hour Prevent certain users submitting no enzyme searches e Let customers view the results of searches run for them without being able to submit searches themselves MASCOT Administration amp Configuration 2007 2010 matrix science MATRIX Mascot security can be very useful especially in a core lab Mascot Security enable disable E Matrix Science Mascot Security Microsoft Internet Explorer File Edit View Favorites Tools Help Back iX iz PL Search zc Favorites O7 s J 9 3 Address e http jt41 dmc mascot cgi login pl Go MA TRIX SCIENCES HOME i MASCOT iHELP Mascot Security Mascot Security Mascot Security is not enabled Copyright 2005 Matrix Science Ltd All Rights Reserved C Inet pub MASCOT bin gt enable_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 MASCO
25. nd 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 1s 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 priority 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 34 Cluster mode Zl Mascot search status page Microsoft Internet Explorer File Edit View Favorites Tools Help Qe o z ix a A Jp Search Sf Favorites a 2 S LJ rel 33 SnagIt e Y Powermarks We A 9 ddress http www matrixscience com x cgi ms status exe v SE d Feb 05 50 25 searches YES Request unmap NO Mem locked NO Number of threads 1 Current YES Cluster Nodes No
26. o delete the file from time to time The searches log is different and you ll probably want to keep all entries indefinitely Best idea is to rename the file periodically For example searches log 20060301 The system will then create a new one automatically If the search log 1s 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 you ll probably want to transfer or rebuild searches log The other important file 1s 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 28 Log files database status E Mascot search status page Microsoft Internet Explorer File Edit View Favorites Tools Help x a A s Search She Favorites oy X LJ rel 33 tf Snagit if Powermarks Mf Address a http koala mascot x cgi ms status exe MASCOT search status page Version 2 1 02 Licensed to Matrix Science Dev 2 processors 4 logical 2 physical Intel processors hyper threading enabled single core CPUs 0 1 2 3 available using 0 1 2 3 0 searches running Search log monitor log error log Error message descriptions Do not auto refresh this pa
27. p javascript void 0 jad Local intranet MASCOT Administration amp Configuration 2007 2010 matrix science Azar 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 You can t disable security from here it has to be done on the server 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 1s 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 Login name Name Password
28. play 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 31 Log files Other useful files e Database compression lt database gt current lt database gt errors e Database taxonomy database current database NoTaxonomyMatch txt e Database statistics database current database stats Web server access and error logs e System event or message log MASCOT Administration amp Configuration 2007 2010 matrix science eae 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 Under Windows the IIS log is in C WINDOWS S system32 Logfiles W3SVC1 The Windows Event Viewer control panel administrative tools allows you to browse Windows system messages 32 Cluster mode External Intranet TCP IP TCP IP EG ro switch TCP IP Mascot master Mascot node 1 TCP IP Mascot node 2 Masco
29. se the keyword search facility The followiNg documents are mainly of interest to system administrators Setup amp Installation Manual fa Release Notes vopyright 2010 Matrix Science Ltd All Rights Reserved Last Updated 03 30 2010 17 14 40 a Local intranet 100 v MASCOT Administration amp Configuration 2007 2010 matrix science AZ The Mascot Installation amp Setup manual 1s linked from your local Mascot home page If you need detailed information on any aspect of Mascot installation or configuration this 1s the place to look Installation amp Setup http t61 jsc mascot pdf manual pdf Windows Internet Explorer ox Ji v e http t61 jsc mascot pdf manual pdf File Edit GoTo Favorites Help w L1 httosljtet jscimascot pdf manual pdf Snagit f od page Gp Tools eA eei Ik 9 Bookmarks E unimod xml E Enzymes E Instruments E Quantitation EHE mascot dat Kj Databases E PARSE E www Kj Processors E Taxonomy l Cluster Kj UniGene Kl Options l Cron KE Log files E Licence 7 Program Reference E a 1 0 File Formats l E 9 Taxonomy E 10 Mascot Daemon E 11 Cluster Mode amp amp 90 3 Collaborate A Sign m ka Sroteinsinresultsfih Li k3 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
30. sp gt Glu substitution Monoisotopic mass 10 008269 10 020735 10 027228 12 036386 12 995249 13 031634 13 979265 13 979265 14 015650 14 015650 Average mass 9 9296 10 0379 9 9273 12 0538 12 9988 13 0418 13 9835 13 9835 14 0266 14 0266 Composition C 6 13C 6 N 4 15N 4 H 2 C 2 Of 1 C 9 13C 9 N 1 15N H 4 C 2 Of 1 H 1 N H 3 C N O 1 H 2 o H 2 0 H 2 C H 2 C Internet MASCOT Administration amp Configuration 2007 2010 matrix science ae The modifications file unimod xml is an XML representation of a public database called Unimod From time to time you should update your local file by downloading the latest file using the links in the Unimod help Mascot configuration Microsoft Internet Explorer Eile Edit View Favorites Tools Help Qs Q ix E JP Search Sf Favorites Configuration Editor Powermarks et A 9 Address amp http Jt41 jsc mascot x cgilms config exe u 1183042968 Mascot Configuration Modifications Phe Ser Phe Tyr Phe Val Phenylisocyanate Phenylisocyanate 2H 5 Phospho Phosphoadenosine Phosphoguanosine PhosphoHex PhosphoHexNAc Phosphopantetheine PhosphoribosyldephosphoCoA Phosphouridine Phycocyanobilin Phycoerythrobilin Phytochromobilin Piperidine Pro Ala Pro Arg Pro Gln 60 036386 15 994915 48 000000 119 037114 124 068498 79 96633
31. t Cluster Topology Mascot node 3 MASCOT Administration amp Configuration 2007 2010 matrix science eae 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 33 Cluster mode Every search is distributed to all the cluster nodes Each node searches a portion of the sequence database 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 Simple socket based communication No parallel operating system required Configuration and program files are distributed and updated automatically from the Master node A cluster behaves and looks like a single server Need dedicated or partitioned hardware Cannot allocate machines dynamically General purpose server farm usually not cost effective MASCOT Administration amp Configuration 2007 2010 matrix science ae 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 a
32. tioned earlier This 1s the starting point for troubleshooting problems especially those connected with database updates When Mascot Monitor first starts there 1s a single entry per database like we see here for MSDB Once a database has been updated there are two entries one for the old file and one for the new like we see here for EST human 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 1s compressed and tested searches can still be submitted to run against the old file Once the new file 1s 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 Mscot monitor takes care of all of this automatically 20 Log files database status E Mascot search status page Microsoft Internet Explorer File Edit View Favorites Tools Help 7 SA Q sax x la pO Search Wi Snagit e Powermarks We A 94 Address g http koala mascot x cgi ms status exe Autorefresh true Show JOBDETAILS Database 1 Which Y Go Mascot Job status Job 2696 Database NCBInr Job Number 2696 Process ID 2996 Task ID 0 User Name Cat R Pillar User ID ig User email leaff mul ch Search title few p
33. urrent searches per user s check boxes and I SEARCH Allow all fasta databases to be searched press Remove Remove Parameter GENERAL View config files using ms status Save changes Came Help window Change details for an existing group Change the users that belong to the group and the tasks that members of the group can perform No changes are saved until the Save changes button is pressed zl 3 Local intranet MASCOT Administration amp Configuration 2007 2010 matrix science JATE When editing a group you can change the name if you wish it is the unique ID that remains constant Users can be added to or removed from the group from this screen This is the list of tasks that are not available or enabled for members of this group So for example if I want to add restrict the number of searches that members of this group can perform I simply click on the task then Add Task In this case I need to enter a parameter as well the maximum number of concurrent searches Note that nothing is saved until you click on Save Changes 12 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 ADM
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