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PEAKS Online Manual 2.0

1. Change for your new password to become active 18 Results Pane he purpose of the Results pane is to display active and past searches A list of user seatch history composed of My search history and Inbox are capable of collecting PEAKS Online generated files My search history My search history provides full details complete with submission date title file used function and database accessed Account Results Search Settings Admin GroupAdmin Monitor My search history Inbox Auto refresh page Send selected results Date Title File Function Database O 4 2008 02 04test cytc pkl PEAKS PIDSwiss Prot O 2008 01 282810 2810 tmp PEAKS PIDSwiss Prot O 4 2008 01 28test cytc pkl PEAKS PIDSwiss Prot O Y 2008 01 28test cytc pkl PEAKS PIDSwiss Prot O Y 2008 01 284 core 2810 tmp PEAKS PIDSwiss Prot O Y 2008 01 288 cores 2810 tmp PEAKS PIDSwiss Prot O 2008 01 27 three 2 core nodes2810 tmp PEAKS PIDSwiss Prot O 4 2008 01 27 two 2 core nodes 2810 tmp PEAKS PIDSwiss Prot O 4 2008 01 270ne 2 core node 2810 tmp PEAKS PIDSwiss Prot O Y 2008 01 04tesssst cytc pkl PEAKS PIDSwiss Prot y Inbox The Inbox acts in a similar manner to that of a standard email address inbox It receives sent PEAKS Online files and notifies users which jobs have been completed When dealing with Viewers and Administrators they can see who provided them with the file 19 Jump to the Assistance section to send these results to a
2. Enzyme configuration PEAKS Online has a number of enzymes that come prepared for immediate use These can be found in the Enzyme list There are many more enzymes that exist and a user may be interested in using during their PEAKS Online analysis Therefore the administrator has the ability to add new enzymes to the list Enzyme list PEAKS Online has a number of enzymes that come prepared for immediate use These can be found in the Enzyme list There are many more enzymes that exist and a user may be interested in using during their PEAKS Online analysis Therefore the administrator has the ability to add new enzymes to the list PTM configuration PEAKS Online has a number of post translational modifications that come prepared for immediate use These can be found in the PTM list There are many more PTMs that exist and a user may be interested in using during their PEAKS Online analysis Therefore the administrator has the ability to add new PTMs to the list PTM list PEAKS Online has a number of PTMs that come prepared for immediate use These can be found in the PTM list There are many more PTMs that exist and a user may be interested in using during their PEAKS Online analysis Therefore the administrator has the ability to add new PTMs to the list 49 An EST database is a division of the GenBank that contains sequence data and other information on single pass cDNA sequences or Expressed Sequence Tags from a
3. PEAKS Online User s Manual BIOINFORMATICS SOLUTIONS INC PEAKS Online User s Manual O Bioinformatics Solutions Inc 470 Weber St N Suite 204 Waterloo Ontario Canada N2L 6J2 Phone 519 885 8288 Fax 519 885 9075 http www bioinfor com support bioinfor com INTRODUCTION TO PEAKS ONLINE lt a EANN A ARM ENDS 4 HOW TO USE TS USERS MANO AL 4 WHAT IS PEAKS ONLINE w CUSTOMIZATION Pim e 3 GETTING STARTED WITH PEAKS ONLINE 2 0 ccccccssssssssssssscessesessssssssesesssessesonens INSTALLATION T EERE 6 Introduction ES Supported processors ned Multiple cores nak 64 Dit SUPP aaa 7 Random Access Memory RAM carroceria REE pi On E KeU PRPA CH tea arepa Rina 8 Hard disk storage Operating system Pre installation INStructiOns RR P 10 Full VersiondnsiallationiGuldeseesasivass RARA OA AAA RA AA RA OA AAA ROR ROR 11 ACCOUNT PANE icisic seri sek FREE EHE E E 16 CREATE AN ACCOUNT iio Forgot password Login email ai LE 17 EM O ds Organization name Account Pane ASSIM carac Evaluation Set up Create an ACCOUNT A A A AR 18 Change DOSS WOLKE seria RA AAA NAAA AAA AAA AAA D M AS 18 RESULTS PANE isis A A A A AA A AAA AA 19 AS PP CR CD
4. Li Kelly Yin kYin more research edu w L jblack amp research ca Ms a m add Update user New user To register a new user to an organization s PEAKS Online community an Administrator will provide required information via the User Info section within User management Full name The person s name shall be entered in the Full name field followed by the Organization s name Login email Enter a valid email address to be used as the login email followed by a passwotd 35 Password To ensure only authorized use PEAKS Online provides encryption protection via a password To ensure no undesired keystrokes during the password setting PEAKS Online requests that the password be retyped for confirmation in the Confirmation field Member of This field indicates the group s which a selected user belongs to It defines the rights the user has and the resources the user can use in the PEAKS Online system Group management The user management system in PEAKS Online is a role based system All resources and rights are assigned to the group role Create a user account in a group to grant the user the privilege to access PEAKS Online As many organizations have many different research labs groups and departments all possibly using PEAKS Online the Group management section will help maintain order Group can be defined according to the research labs research groups and departments The administrator can also define t
5. amount of the memory However there is a work around On a multiple processor server multiple PEAKS Online instances can be installed Each instance will bind to a distinct IP address All the instances form a cluster and work together The only requirement on the server is to configure multiple IP addresses 64 bit systems 64 bit systems have a huge addressing space and there is almost no limitation for the memory PEAKS Online can use as much memory as the customer specifies to do the computation Customers can just add RAM to increase the capacity of their PEAKS Online server On a multiple processor server PEAKS Online can run multiple processing threads in one PEAKS Online instance instead of the multiple instances on the 32 bit system In practice we found that 2GB RAM per processing thread may be a good choice For example a dual processor server should come with 4GB RAM Hard disk storage The amount of hard disk storage space required for PEAKS Online server is determined by the following factors PEAKS Online program files The PEAKS Online program files require less than 100MB per instance It is still very small compared to other factors Sequence database The size of the sequence database depends on the customer s requirements The more databases the customer wants to search against the more storage space is needed Usually the databases will occupy several GB to hundreds of GB disk space Result file
6. maximize ease through the PEAKS Online software Available modifications The Available modifications table presents a complete list of PTMs that any user can set as either fixed or variable modifications Click the box inline with the desired modification o Click Set fixed gt to set this as a fixed modification Or o Click Set variable gt to set this as a variable modification Multiple PTMs of the same type fixed or variable can be selected quickly by e Clicking each desired modification box e Then clicking the Set fixed gt or Set variable gt button o Once set the modification s will appear under the Selected modification list to the right If a user hovers the cursor on a PTM a PTM detail tooltip dialog will show up after 1 second Unset selected modifications To unset a selected modification e Click the box in the Selected modification list that corresponds to the undesired modification and click lt Unset PTM s Contact your Administrator to permanently add PTMs not currently listed 29 Remove selected modifications To remove a selected modification click the box in the selected modification list that corresponds to the undesired modification and click lt Unset PTM s To remove multiple PTMs simply click each box corresponding to the undesired Selected modifications and click lt Unset PTM s Submit To send the search parameters data file
7. specific party Jump to the Assistance section to remove selected searches from the queue Search Settings Admin GroupAdmin Monitor My search history Inbox Auto refresh page Send selected results Date Title File Function Database Owner y 2007 12 18 Pesti 014 CSIS 91923 anz PEAKS PID Swiss Prot Brian Persoon Open Save file In either tab My search history or Inbox to open a file simply click the date for the html report to appear In PEAKS Online users can download the ANZ file at anytime they want by simply click on the download result file link the green arrow Auto refresh page To ensure that users are aware of a status of a search currently being processed an Auto refresh page option box located to the left can be checked to update the page every 5 seconds This ensures completed jobs are sorted into either My search history or the Inbox quickly after completion Send selected results As PEAKS Online has been configured with each user s email address users alike can send via email for notification and internally to PEAKS Online Inbox results to one another for examination Results Search Settings Admin GroupAdmin Monitor My search history Inbox O Auto refresh page Send selected results Date Title File Function Database v 2008 02 04test cytc pkl PEAKS PIDSwiss Prot v 2008 01 282810 2810 tmp PEAKS PIDSwiss Prot O Y 2008 01 28test cyte pkl PEAKS PIDSwiss Prot O Y 20
8. AMD Athlon 64 e Intel Pentium 4 processor AMD Sempron Intel Core 2 Extreme AMD Phenom Quad Core processor Processors e Intel Core 2 Duo processor Intel Core 2 Quad processor Multiple cores The most recent Intel and AMD processors contain multiple cores A multiple core processor is like putting multiple processors into one chip It reduces the cost and boosts the performance In our internal testing PEAKS Online can run nearly twice as fast on a dual core processor as on a single core processor PEAKS Online is licensed on a per thread basis This means that one must purchase a license for each CPU core that will run PEAKS Online But don t worry price per core drops off rapidly with volume 64 bit support Both Intel and AMD have their own 64 bit processor technology Intel EM64T AMD AMD64 32 bit applications can also run on these processors If the customer purchases 64 bit processor servers PEAKS Online can run in either 32 bit mode or 64 bit mode We strongly recommend running PEAKS Online on 64 bit mode especially in a high throughput solution Random Access Memory RAM PEAKS Online is a memoty intensive program The amount of physical memoty has critical effect on the capacity and speed of PEAKS Online 32 bit systems Due to the limitation of 32 bit Sun JVM PEAKS Online can only use approximately 1 5GB per instance That means on a 32 bit system with 4GB RAM PEAKS Online may waste half
9. a protein or EST database Thus it will need to be download from the Internet and PEAKS to be informed where the database is located PEAKS provides the Database configuration as a tool to easily set this up Also from here we can edit a database s properties load a new database or remove an existing database PEAKS Client uses the databases configured on the PEAKS Online server PEAKS Online will treat NR and Swiss Prot databases as two special databases These two databases are the most commonly used public databases therefore PEAKS Online can support these special taxonomy files PEAKS will not accept taxid taxdmp or speclist files from other databases To configure a database once the database is located on the internal network and in FASTA format the administrator will add the database to PEAKS Online 32 Jump to the Assistance section to add update or remove enzymes Database list Account Results Search Settings Database configuration E v NCBI nr Swiss Prot Apply GroupAdmin Monitor Path home cluster db nr nr fasta Path home cluster db sprot uniprot_sprot fasta Taxonid home cluster db nz gi taxid protdmp gz Taxdmp home cluster A db nx taxdmp zip Customer database Database list E BLG Database RS Group O xsmYH Public L IPLHUMAN Public C IPLMOUSE Public L Lactobacillis Mi 5 i lt Speclist home custer db sprot speclist xt
10. and database to the PEAKS Online cluster press the Submit button If a job has been submitted that a user wishes to cancel click on Results pane in the particular file in the Searches in the queue section then click Remove selected searches Add Taxonomy The Taxonomy tree is comprised of a list of biological taxa in which a researcher can strictly limit their results Select a particular taxonomy by clicking its name in the Taxonomy tree list Confirmation of this selection is given by its appearance in the Selected Taxonomy window Multiple taxonomy selections 9 Choose the database are available and Swiss Prot ot sprot bi ossible simply b P ao aes Selected Taxonomy Taxonomy tree repeating this process Archaea Aeropyrum pernix J Remove Taxonomy Methanococcus jannaschii To remove a taxonomy Other Archaea selection from the Bacteria ec 99 Selected Taxonomy mS 2 list click the 3 located to the left of O Identify PTMs in known proteins the taxonomy name The list will refresh with the removal of this selection 30 Settings Pane he Settings pane allows users to organize the Results pane User options include declaring Search results are publicly available as well as specifying the Result time range Once Settings have been selected click Apply changes Account Results Search Settings Admin GroupAdmin Monitor Search results
11. are publicly available Result time range Show results within 100 days 0 all results Apply changes Search results are publicly available By selecting this option clicking the box to the right any person with the result URL can access the output even if they are not PEAKS Online users No login will be required If this field is unchecked the results are private Only those PEAKS Online users whose inbox contains the results can access them Result time range This option allows users to configure their own preferences by displaying either all results indicated by the number 0 zero or a more specific time frame thus to Show result within 2 days If no value is entered a default of 0 will act and display all results 31 Jump to the Assistance section to configure a database and add a new database Jump to the Assistance section to add a customer database and removed selected databases Admin Pane he Administration pane allows a representative of an organization to configure such things as databases enzymes post translational modifications manage users and groups as well as some miscellaneous Misc settings Database configuration New database PEAKS Online requires a protein or EST database in FASTA format to identify protein candidates Since databases are being constantly updated and each organization has their own database preference PEAKS Online does not provide
12. back into this document in the event that there are any difficulties experienced a BSI engineer will be well prepared to troubleshoot the issue 1 Plan the server topology If you are working with multiple servers i e a cluster select one server as the WebServer main server Otherwise if many servers have the same hardware configuration pick the most powerful one as the WebServer If you only have one server there is no choice simply install all PEAKS Online components on the server 2 Create a user account for PEAKS Online on all servers 3 Install JDK 1 5 on all servers This version of Java can be downloaded from http java sun com javase downloads index_jdk5 jsp After the installation create an environment variable JAVA_HOME to point to the Java installation directory Make sure the JAVA_HOME bin directory is in the system s PATH You can test that this is ok by typing java version at a command prompt Note Under Linux the full path name of the Java installation directory should not contain any blank Spaces 4 Install MYSQL server 5 0 or above on the WebServer If the PEAKS Online cluster has more than 6 nodes we recommend installing MYSQL on a separate dedicated server MYSQL can be found at http dev mysql com downloads a Create a user password for PEAKS Online use and grant all privileges to that user For example the following command will create user x password y with all privileges GRANT ALL PRIV
13. been entered click Add Update enzyme to add it to the Enzyme list 42 Note B uilt in enzymes can not be modified Note Built in enzymes can not be modified Update enzyme To Update or modify an existing enzyme Click the particular enzyme in the Enzyme list The name will appear in the Name text box as well as the Digestion rules will appear Modify the Name or Digestion rules as desired e Click the Add Update enzyme button Remove selected enzyme To remove an enzyme from the Enzyme list Select the box corresponding to the appropriate enzyme e Click the Remove selected enzyme button to eradicate it from the list PTM configuration New PTM To create a new PTM li Click on the New PTM button 2 Give it a name and abbreviation one that easily explains its form function 3 Enter the mass neutral loss both in Daltons 4 Proceed by entering details regarding where the residues will be modified Everywhere N terminus C terminus Middle only as well as possibly a Rule for other future user understanding Once complete press Add Update PTM 6 The recently added PTM will appear on the PTM list wn 43 Note Built in PTM can not be modified Note Built in PTM can not be modified Update PTM To Update or modify an existing PTM Click the particular PTM in the PTM list The details will appear on the left in the text boxes according to their purpose To chang
14. e The database s properties will be shown on the left e Change the properties to the new value 41 Click add update database to make the change take effect Remove selected database To remove a database e Click the box beside the undesired database in the Database list e Press Remove selected Database o It will be removed from PEAKS Online As this will not permanently remove or delete the database the database will be able to be used again in the future if it is re entered into the Database list using the standard database configuration instructions Enzyme configuration New enzyme To create a new Enzyme 1 Click the New enzyme button 21 Give the Enzyme a name one that easily explains its form function 3 Enter the Digestion rules that correspond in the following boxes The text boxes on the left are for residues at the end of a peptide the boxes on the right for those at the start of a new peptide Use set brackets around he residue to denote any amino acid except the ones enclosed in these brackets The letter X can be used to denote any residue 4 Further a user can specify a more particular preference for handling this enzyme simply by clicking on button of their preferred choice a Find peptides that satisfy the above at both ends b Find peptides that satisfy the above only at C terminus and or peptides that satisfy the above only at N terminus 5 Once each setting has
15. or absence of the PTM for each occurrence of the amino acid residue in its analysis Selected modifications Whether non one or multiple fixed and or variable modifications ate expected this section confirms which have been properly selected by the user 24 Note that only one position can be specified per entry However multiple entries can be strung together using commas User defined PTM Users can define Post Translational Modifications PTMs and PEAKS Online will always record the search parameters used in the latest search and use them as the default parameters in the search page Future use of these same PTMs will require users to re enter the modification details or be entered by the group or system Administrator for PEAKS Online Fixed Variable user defined PTM The dialogue box to the right of the field title is the Fixed User defined PTM or Variable User Defined PTM input area Here user defined fixed PTMs can be entered The format is monoisotopic mass change residue list position on the residue no brackets The monoisotopic mass change is the additional mass to be added to the residue The residue list is the list of amino acid residues that are effected by the modification The position refers to the placement of the modification on the amino acid residue C means the modification is on the C terminus N the N terminus and A is for anywhere and is non specific Fixed and Variable Us
16. prior written consent of BSI General These Terms and Conditions constitute the entire agreement between BSI and you pertaining to the subject matter hereof We may in our sole discretion revise these Terms and Conditions from time to time You should periodically visit this page to review the current Terms and Conditions so you are awate of any revisions to which you ate bound 60
17. queued as well as details regarding the PEAKS log file these are located in the Monitor pane Account Results Search Settings Admin GroupAdmin Searches in the queue Auto refresh page Remove selected searches Status Date Title File Owner O running 2008 02 05 16 12 03 test cytc pkl mxie bioinfor com View log file gio A view 14 10 07 146 INFO STDOUT I am the last one do cleanup 14 13 07 173 INFO STDOUT check the taskList 14 14 07 184 INFO STDOUT check the taskList 14 15 07 440 INFO STDOUT check the taskList 14 16 07 749 INFO STDOUT check the taskList 14 17 08 060 INFO STDOUT check the taskList 14 18 08 367 INFO STDOUT check the taskList 14 19 08 676 INFO STDOUT check the taskList 14 20 08 983 INFO STDOUT check the taskList 14 21 09 293 INFO STDOUT check the taskList 14 22 09 604 INFO STDOUT check the taskList 14 23 09 914 INFO STDOUT check the taskList 14 24 10 224 INFO STDOUT check the taskList 14 25 10 531 INFO STDOUT check the taskList 14 26 10 839 INFO STDOUT check the taskList 14 27 11 147 INFO STDOUT check the taskList 54 Searches in the queue Searches in the queue show which tasks are waiting to be processed There is an option to automatically refresh the queue Auto refresh page details This updates about every 5 seconds to give you the most up to date search details Additionally there is a remove selected searches tab which can be used if multiple runs of the
18. same file using the same parameters and databases have been submitted consequentially delaying other jobs View log file The log file keeps a written account of PEAKS Online s actions It is highly effective in recording exactly what is being performed by PEAKS As Log file is constantly being updated with each new process completed it is relevant to select a particular section of the log file for examination rather than the entire file The View the last __ KB section is designed to quickly identify the current stage of PEAKS processing 55 About Bioinformatics Solutions Inc BSI provides advanced software tools for the analysis of biological data ioinformatics Solutions Inc develops advanced algorithms based on innovative ideas and research providing solutions to fundamental bioinformatics problems This small adaptable group is committed to serving the needs of pharmaceutical biotechnological and academic scientists and to the progression of drug discovery research The company founded in 2000 in Waterloo Canada comprises a select group of talented award winning and intelligent developers scientists and sales people At BSI groundbreaking research and customer focus go hand in hand on our journey towards excellent software solutions We value an intellectual space that fosters learning and an understanding of current scientific knowledge With an understanding of theory we can focus our talents on providing so
19. step by step his section of the manual will guide us through the process of registration and configuration of PEAKS Online If we run into any problems we can contact technical support at support bioinfor com This section of the user s manual is applicable only to those customers who have purchased PEAKS Online for use with an in house server Those evaluating before purchase need not install any software as the PEAKS Online web demo is already installed and hosed at www bioinfor com peaksonline Installation Introduction Note If you are using more than4 PEAKS Online can run on almost any recent high specification server or desktop PC iden equipped with Intel or AMD processors The server can be a single processor server a dual costs are lower than the equivalent multi processor box i e 4 dual CPU boxes are less expensive than one 8 CPU box processor server or a server with even more processors Note PEAKS Online currently does not support Itanium processors This is because Itanium processors are not supported by Sun JVM Supported processors PEAKS Online support most Intel and AMD processors Below are the lists of processors we support Supported processors Intel Processor AMD Processor Intel Xeon processor Intel Xeon processor MP AMD Opteron Intel Pentium D processor AMD Athlon 64 FX Intel Pentium 4 processor AMD Athlon 64 X2 Dual Core HT
20. to BSI engineers due to security reasons we suggest using WebEx to let BSI engineers help in the installation process Full Version Installation Guide Note JDK 1 6 Java 6 is not supported by PEAKS Online Please make sure JDK 1 5 Java 5 is installed These instructions are written under the typical scenario of a 3 server deployment the Portal Server main server IP 192 168 1 100 the Cluster Master node IP 192 168 101 the Cluster Slave node IP 192 168 1 102 1 Download both installers from e http www bioinfor com tmp polinstaller jar http www bioinfor com tmp polupdate jar If you are using Windows the jar file often automatically saves as zip file if so please rename it back to its native jar format Copy these jar files to the target directory for example d peaksonline test 2 Create two databases in MYSQL with the name peaks and jbossdb using your MYSQL PEAKS user account 11 3 On the Portal Server in command line change to the target directory and run the command Proceed by following the on screen instructions Below shows a screen shot for this example deployment in grey Note a There is no need to configure any FASTA databases at this moment b When choosing the installation type choose 2 Portal server in multiple server deployment If only one computer will be used for PEAKS Online choose 1 All in one c Amount of memory specifies how much memory PEAKS Online will
21. 08 01 28test cytc pkl PEAKS PIDSwiss Prot Y 2008 01 284 core 2810 tmp PEAKS PIDSwiss Prot F1 amp 2008 01 288 rnras 2R10 tmn PFAKS PIDSwiss Prnt Searches in the queue As many jobs may be submitted before a processing file has been completed a task queue clearly displays the order of files that will be processed after the current file s completion 20 Results Pane Assistance This section will lead users through step by step instructions which should be followed to maximize ease through the PEAKS Online software My search history To send these results to a specific party e Select the box that corresponds to the desired file Multiple files may also be sent by selecting multiple boxes Press Send selected results An email prompt will appear requesting the user enter the destination email address Be sure that the recipient address has been registered with PEAKS Online or an error prompt will appear and advise you of this issue Qo 0 Send selected results Select the corresponding result boxes you wish to send Click on this text to prompt the email window to appear Enter the email address of a registered PEAKS Online account Press Send The message will be sent to the recipient s email account for notification purposes as well as the files will automatically appear in the user s PEAKS Online account Inbox located in the Results Pane Remove selected searches To remove a search in the search que
22. 1000 Please specify how many CPUs Cores are in this server 2 License Agreement Do you accept the license agreement to install the product yes no yes Extracting PeaksOnline components done Installing JBoss done Configuring PeaksOnline done Deleting temporary files done PeaksOnline Server has been successfully installed 5 On the cluster slave nodes in command line change to the target directory and run the 13 command java jar polinstaller jar install config A screen shot can be seen below in grey Note Choose 5 Cluster slave as the installation type D peaksonline test gt java jar polinstaller jar install config Please choose the installation type 1 All in One Install all components in one server 2 Portal server Install the portal server for multi server installation 3 Process server Install the process server for two server installation 4 Cluster master Install the master node for the cluster installation 5 Cluster slave Install the slave node for the cluster installation Installation type choose 1 to 5 5 Cluster nodes 0 192 168 1 100 1 192 168 1 101 2 192 168 1 102 Please choose the address for this server 0 2 2 Please specify the amount of memory PEAKS Online may use 1000 Please specify how many CPUs Cores are in this server 2 License Agreement Do you accept the license agreement to install the product yes no yes Extracting PeaksOnline component
23. E ope 48 Select a group Database configuration New database Enzyme coni SUTTON 49 PTM configuration GroupAdmin Pane Assistance Database configuration ING W CaaS Caso tients ud N E E A A cad Remove selected database ENTIME CON TULA A ASA A elena NeW VAM Update enzyme Remove selected enzyme PTM configuration Update re Refnove selected TNE sauce NEM EE ME MEE a MONITOR PANE p AA AA A 54 Searches in the queue View log file ABOUT BIOINFORMATICS SOLUTIONS INC cccccscscssssssscscssssessssssscsssssssssscesssessssssscscesssssssessssesssesssssessssssssessssssecesssessssasesesasasees 56 PEAKS ONLINE TERMS OF SERVICE Introduction to PEAKS Online EAKS Online means high throughput on a shared resource It is fully parallelized with p the ability to run on any cluster or multi CPU machine PEAKS Online returns auto de novo sequences and identifies peptides proteins given MS MS tandem spectral data The results are displayed in HTML via a built in web server Links to the results are e mailed to the user after analysis This means that everyone in an organization who has a browser an e mail address and access to the cluster can submit data and view results To get the ful
24. ILEGES ON TO x IDENTIFIED BY y WITH GRANT OPTION b Add the following lines or change the value if the settings are already in the file to mysqld section of the my cnf Linux or my ini Windows file tmp table size 90M max allowed packet 32M binlog do db peaks 5 Restart MYSQL server to make the changes take effect 10 6 Install a SMTP mail server somewhere on the network and create an email account fot PEAKS Online Most customers already have a mail server for their daily work That server can be used if it is a SMTP mail server 7 If the target operating system is Linux the Xvfb X Virtual Frame Buffer must be installed on the WebServer so that users can see images of their spectra Please install it and add it to the PATH environment variable There are a number of specific versions depending on the operating system A simple Google internet search engine search will help find the right one 8 Put all FASTA database files into a directory on the WebServer which PEAKS Online can access If you want to use the NCBI nr and or Swiss Prot database the corresponding taxdmp and taxonid files are required 9 It is recommended that a BSI engineer be allowed to conduct the installation remotely For an installation on a a Linux system the SSH and TCP 8080 ports need to be opened on the firewall b Windows system remote desktop access must be granted 10 If the direct access to the server can not be granted
25. Identify PTMs in known proteins To quickly search a set of sequences without having to configure a database select the Identify PTMs in known proteins option and paste or upload the sequences on the search form In either case protein sequences must be in FASTA format In FASTA format for each protein we have a header line beginning with the greater than symbol and usually optionally containing a unique identifier gi or accession number and a description of the protein For instance protein MYPROTE NSEQUENCEW THNOSPACES gt M other protein THENEXTPROTEI NSEQUENCEAGAI NW THNOSPACES It s important to make sure there are no illegal characters in the protein sequence and that the header begins with gt the greater than symbol If we already have a file containing these sequences it s recommended to configure them as a database so they can be easily re used remember the database can still be kept private But to do a single quick search we can upload the file here Just click the Browse Button and choose the file PEAKS will not search both the pasted sequences and the uploaded file Please use one or the other Reset This button will erase the FASTA sequences and uploaded file from the Identify PTMs in known proteins section This is not a Reset button for the entire Search pane 28 Search Pane Assistance This section will lead users through step by step instructions which should be followed to
26. Ms that any user can set as either fixed or variable modifications If a user hovers the cursor on a PIM a PIM detail tooltip dialog will show up after 1 second 23 Jump to the Assistance section to remove selected modifications from the search Modification Available modifications Selected 1 Oox O Palmitoylation O Phospho lt Unset PTMs PTM detail Uer defined Name Phosphorylation PTM Abbreviation Phospho Mass 79 966331 Neutral loss Function AAA Residues that can be modified Everywhere STYHCD N terminus C terminus Middle only propr Rule C isin only Prokaryotes Adding new modifications As an administrator of the PEAKS Online system if you wish to add modifications to the Available modifications list examine the PTM configuration instructions in the Admin pane Fixed modification This type of modification refers to amino acid residue modifications or PTMs post translational modifications which are always present any time that particular amino acid appears in the protein Therefore the molecular weight of the amino acid residue is fixed for all its occurrences in the protein Variable modification This type of modification refer to amino acid residue modifications or PIMs post translational modifications that may or may not be present when the amino acid occurs in a protein PEAKS Online will take into account either the presence
27. NA sequences or Expressed Sequence Tags from a number of organisms Admin Pane Assistance This section will lead users through step by step instructions which should be followed to maximize ease through the PEAKS Online software Database configuration New database les To configure NR or Swiss Prot databases a user will need to check this box to enable editing properties Once the name path taxid taxdmp fields are entered Click apply button to save the changes To change the configuration simply edit the fields Click apply to make the change take effect CaS M To configure a database once the database is located on the internal network and in FASTA format the administrator will add the database to PEAKS Online start by giving the database a name something relevant and easily identified enter the path manually in which PEAKS Online will use to navigate to access the database Customer database For customer databases to set a new database Click on the New db button Give the database a name Direct PEAKS Online to where the database can be accessed either manually Select the database format using the drop down menu If this is an EST database click the box to the left Once configured click Add Update Database to add it to the list of useable databases SAU E SES To change the configuration of an existing database e Click on the database name in the database list
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29. S RESOURCE IMPORTANT NOTICE TO YOU These Terms and Conditions of Use the Terms and Conditions govern your use of the PEAKS Online product including without limitation use of all underlying software all content data images information and other materials posted on or available through this resource collectively PEAKS Online These Terms and Conditions are in addition to any other agreement you may have with BSI including any agreement governing your use or your organization s use of BSI products or services Bioinformatics Solutions Inc referred to as BSI we us or our herein hereby grants you a nonexclusive license to use PEAKS Online As a condition of your use of this resource you warrant to BSI that you will not use PEAKS Online for any purpose that is unlawful or prohibited by these Terms and Conditions You may not reverse engineer deconstruct disassemble decompile or create derivative works based on PEAKS Online or any software or technology underlying or provided through PEAKS Online If you breach any of these Terms and Conditions your authorization to use this resource shall automatically terminate The contents of PEAKS Online may not be distributed modified reproduced or used in whole or in part without the prior written consent of BSI except that you may download data analysis results from PEAKS Online provided you keep intact all copyright trademark and other proprietary notices and comply with an
30. Taxdmp home cluster db sprot tax mp zip i Database info Name IPLHUMAN Path home cluster db ipi ipi HUMAN v3 32 fasta Format IPI O This is an EST database Add Update Database Remove selected Database This is a complete list of databases configured in the entire PEAKS Online system Enzyme configuration PEAKS Online has a number of enzymes that come prepared for immediate use These can be found in the Enzyme list There are many more enzymes that exist and a user may be interested in using during their PEAKS Online analysis Therefore the administrator has the ability to add new enzymes to the list Enzyme configuration Enzyme list Semi Asp N Built In Semi Asp N N terminal Glu Built In Semi Chymotrypsin Built In Semi CNBr Built In Semi Glu C bicarbonate Built In Semi Glu C phosphate Built In Semi Lys C Built In Semi Pepsin pH 1 3 Built In Semi Pepsin pH gt 2 Built In Semi Proteinase K Built In Semi Trypsin Built In A lt Enzyme info Name semi Trypsin Digestion rules residues at the end of a peptide start of a new peptide rK L Use set brackets around a residue to denote any amino acid except the ones enclosed in these bracket Use X to denote any residue O Find peptides that satisfy the above at both ends Find peptides that satisfy the above only at C terminus and or peptides that satisfy the above only at N ter
31. Ue Ma GER CEU ed PER EN sind adams BISA ag den tA Wand UICE AREA dE hac TR ened oe 19 Inbox SEAT CHESTE GUC E P 20 Results Pane Assistance My search history Remove selected searches AAA AAN MARIE ACREAGE ORG RIO AAA 21 SEARCH PANE o I 22 Search Uileann anaona ASEA ias ae Dat 23 EM di 23 Allow up to 23 Modification HO 23 User defined PTM 25 dinero ain irene ASG a Aen 25 PU m 26 Merge tol Init n siddME D M H Fragment tol Precursor massa asilo ERR RARIOR UR pP EA ENAT S HORE IR M ERO APR EERULS RACE BERE RECEN VPUEPREER EDS NIKEI EUREN p S Choose the database a eetticceie too ttgicetedebesue on 27 Identify PTMs in known proteins 28 Search Pane Assistance vg Available modifications 29 Unserselecied modifications iie PRESE btc be M cor pau beue SE 29 NO UTVACIITUrm bum 30 SUD INL senec opE Eire AA ir 30 SETTINGS PANE re C 31 Search results are publicly available Result TIME TAN M 3d ADMIN PA d ope Hm 32 Database vonfiguration New databas Criando 32 Database lists tae ane AA eae 33 En
32. ail A working email address serves in PEAKS Online as a user name Benefits of this approach allow a destination to where results and notifications can be sent additionally to the PEAKS Online internal account Full name This is a designation that will tell administrators users viewers who the results have been sent from in an e mail message Organization name The label given to the institute whether academic government or corporate which will help it be identified from other associations 17 Account Pane Assistance This section will lead users through step by step instructions which should be followed to maximize ease through the PEAKS Online software Evaluation set up Create an account A new User will need to create an account in order to provide the BSI cluster with one s data To do this da 2 Click the link on the opening page that directs users to Sign up for PEAKS Online Free The user will need to fill out the sign up form and accept the terms of service A email will be sent to the provided email account which a user must click on the link with in the email in order to activate this account Now the account is ready for testing Evaluating users only Change password Ore pa ps To change a password the user or administrator of the account can Click Change Password Enter the old password followed by the new passwotd The new password is requested twice for confirmation Press
33. ame or Digestion rules as desired Click the Add Update enzyme button Remove selected enzyme To remove an enzyme from the Enzyme list Select the box corresponding to the appropriate enzyme e Click the Remove selected enzyme button to eradicate it from the list PTM configuration New PTM To create a new PTM Click on the New PTM button e Give it a name and abbreviation one that easily explains its form function e Enter the mass neutral loss both in Daltons e Proceed by entering details regarding where the residues will be modified Everywhere N terminus C terminus Middle only as well as possibly a Rule for other future user understanding Once complete press Add Update PTM O The recently added PTM will appear on the PTM list Update PTM To Update or modify an existing PTM Click the particular PTM in the PTM list The details will appear on the left in the text boxes according to their purpose 52 To change a particular detail Click in the field you wish to change Enter the new value Once complete press Add Update PTM The recently updated PTM will now appear on the PTM list Remove Selected PTM To remove a PIM from the PTM list Select the box corresponding to the appropriate PIM Click the Remove selected PTM button to eradicate it from the list 53 Monitor Pane EAKS Online provides a solution for supervising the tasks currently
34. at the relevant details appear on in the User Info and Member of section e Make the necessary changes to any field including groups by selecting the preferred new preference and unselecting the previous status Remove user To remove a user Locate and select the box that corresponds to the particular person Click Remove selected user 45 Group management Group list To select all members in a category such as Group users Click Select all located just below the Group users title bar O The same option can be carried out to deselect all by clicking Deselect Press the Add Update Group button in the bottom right corner of this tab Add Update group To create a new group 1 Click on the New group button 2 Type in the new Group Name in the Group Name field 3 Click the Add Update group button located just below the Group list Remove selected group To remove a selected group Click the group s box to the left of the Group name in the Group list e Press Remove selected group Group database To assign a database to a particular group Select the box beside the group s name in the Group list Select the box beside the particular database name in the Group databases section Press Add Update group O As with other sections a Select all and Deselect all option is available for administrative convenience 46 Group enzyme Assigning an enzyme to a par
35. ault license directory on the Portal Server there is a reg log dat file Copy that file to a computer with internet connection and use a web browser to launch the page http www bioinfor com OnLineRegistration php Fill in the information required and upload the file You will get an automatically generated email containing the license file very shortly Copy that license file to the same directory as reg_log dat file located Note If it is an All in One installation the reg log dat file is in d peaksonline test jboss server all license directory 11 In Internet Explorer go to http your portal setver 8080 peaksonline You will see the login page in about 10 seconds Use the login name admin and password peaksonline to log in to PEAKS Online 2 0 Go to admin pane by clicking the admin link on the top banner and then click the Misc settings tab at the bottom Set all desired settings and ignore the Disable security and Blocked email domain for sign up since these settings will not be in use For the log file setting in Windows just ignore it In Linux Unix type in jboss bin tmp log Click the Apply changes button to save all the settings 12 There is a User s Manual link at the bottom right corner of the web page You can configure the FASTA databases enzymes and PTMs by following the instructions in the manual Note All databases enzymes and PTMs are not assigned to any groups by default The administrator will need to assig
36. e a particular detail e Click in the field you wish to change Enter the new value Once complete press Add Update PTM The recently updated PTM will now appear on the PTM list Remove Selected PTM To remove a PTM from the PTM list Select the box corresponding to the appropriate PIM Click the Remove selected PTM button to eradicate it from the list User management Add a user To create a new user in the PEAKS Online community as an administrator in the Admin pane e Click New User e Enter the specific details of the user such as O email address O password O full name o etc Optional the check box Force change password at next login to have the user change create their own password when they log into this account next Membership to a group is given simply by checking the relevant group boxes below e Click Add Update user 44 Disable user access To temporarily restrict a person the Administrator may select the Disable button when a specific username is being viewed Force password change To allow a user to change their password upon first logging into PEAKS Online e Select the Force change password at next login o Click the appropriate Status of the user O Whether that be Administrator User or Viewet e Click Add Update user Update user To update a person s profile in PEAKS Online as an Administrator e Select the Affiliate s name so th
37. er defined PTM Examples Single entry 23 5 AHS N Multiple entries 12 32 ANS N 23 1 K A 8 GH C 123 FPDTW N Allow up to variable PTMs per peptide This allows users to restrict the number of variable PTM that will appear on any given peptide Function The purpose of PEAKS Online is to identify proteins and peptides This can be accomplished by searching through databases and de novo sequencing The collective task of performing de novo sequencing and protein identification is referred to in PEAKS Online as PEAKS Protein ID Users with a preference can choose from the following function options find the de novo sequences not from database results PEAKS Protein ID from database results Further if a user has the existing de novo results they may provide them to the cluster for examination use existing de novo results 25 De novo sequencing By selecting this option only the auto de novo sequencing is performed The peptide sequence tags will be returned for each spectrum PEAKS Protein ID This option tells PEAKS Online to do auto de novo sequencing and protein identification Peptide sequences and a list of protein possibilities with their confidence scores will be returned in the results This is the most highly recommended function in order to return the most accurate results Use existing de novo results This option will skip the de novo step and use the existing PEAKS de novo sequencing results from a pr
38. evious run to identify the possible protein matches in a specified database This option is intended for when a user is loading PEAKS native ANZ file Preprocess When dealing with MS MS data it is often useful to remove outliers smooth detrend or otherwise treat the data to make it more tractable for analysis and estimation purposes PEAKS Online provides effective for carefully and accurately exclusion detrending and filtering Do preprocess If checked PEAKS Online will preprocess the spectral data before doing de novo sequencing or protein identification Be careful here if the data has been preprocessed preprocessing again will make the results less correct Enable Filter By enabling the filter feature data of insufficient quality can be easily removed Merge tol If the m z ratio s of precursors from two or multiple spectra are quite close to each other within the tolerance they can be merged into one spectrum The resulting spectrum 26 intensity will be the result of the 2 intensities added together In PEAKS Online a user can set this value in Da Daltons Instrument PEAKS Online was trained to use different internal parameters with different instruments Choosing the instrument that the data originated from will improve the PEAKS Online output results Parent tol Parent tolerance is the peak matching error tolerance from the service scan of the parent ion It determines how much random and syste
39. exclusively use on thi computer in MB In a 32 bit system the maximum possible value is around 1500 In 64 bit system use 2000 or more if possible d Number of cores This specifies how many processing threads PEAKS Online will launch on this node On each node the maximum number of processing threads should not exceed the number of cores The total number of processing threads on all nodes should not exceed the number allowed in the license For example if the license is a 5 CPU license up to 4 processing threads on cluster nodes are allowed since there is one thread running on the Portal server e The install config file will be created in the directory It records all the information the user has input Please copy this file to the target directory on other PEAKS Online computers for later use f If it is an All in One installation go to step 6 12 The sender s email address abc abc com The admin s email address abc abc com Portal server internal ip host name 192 168 1 100 Portal server external ip host name 192 168 1 100 Number of jobs can be submitted per day for non privilege IP default 5 5 Please choose the installation type 1 All in One Install all components in one server 2 Portal server Install the portal server for multi server installation 3 Process server Install the process server for two server installation 4 Cluster master Install the master node for the cluster installation 5 Cluster slave In
40. he groups according to the actual roles in their production environment For example some junior fellows can only access low confidential resources but for senior researchers they may access some high confidential resources PEAKS Online has three built in groups Administrator group Users group and Viewers group User management l Group list Group Name Select all Deselect all Selectall Deselect all aPerson bioinfor com BLG Database RS Group Lj Ahuman Person Ao bPersoon company com KSMYH Public O Brian Persoon Pe ParaCit Internal 5 L cPersonne university edu L Christina iae O dMenschlich pharma com CSRR Public O sito Menschlich O Edward biotechcamp com HAAR Public ee O Frankie colleycross com RER USAS Li O gPessoa proteinstudy com IPI Mouse Public Gordon Pessoa O HPPapulinet IPI Human Public Henry Mepcona O iRen amp SMIS ca Lactobacillus Mi5 Ira Ren O jninshou bioinfor com MoonLD JamesMorrison L Jennifer Ninshou O kYin more research edu E WMW 1 BJohnson E O Hepplel mass spectrom net YSMANL Fells LJ Lindsay Menselijk 3 O angusyoung peakpick ca M IYWB Ug It v ai 3 O nsixx proteomehome ks z mr m ge _ EES 36 Group list The Group list shows all groups in the PEAKS Online system Click on the group name in the Group list to display detail information about the group across six different sections 1 Group users All users belong to the gro
41. it Reset 22 Jump to the Assistance section to set available modifications to the search Search title The Search title will act as the label or name of the search and can quickly inform viewers or other users what the file contains Data file Use the Browse button to navigate the desired file to be processed to PEAKS Online The format of file can be pkl dta mef mzxml anz and zip zipped dta files Enzyme Select the name of the enzyme used to digest the proteins before mass spectrometry from the drop down menu If the enzyme of choice does not appear in the list contact your group administrator or PEAKS Online administrator to add it to the list or select none Allow up to missed cleavages The missed cleavages section allows the user to manually define the maximum number of missed cleavages between peptides To set this option to zero would suggest there are no partial fragments and if correct result in a very high score Due to many samples often containing fragments from other peptides it is suggested that a user set this field to between 1 and 3 missed cleavages That said the higher the number of cleavages missed may increase scope but it may also decrease sensitivity Modification Two types of modifications exist fixed and variable modifications Both can be used as search parameters in PEAKS Online Available modifications The Available modifications table presents a complete list of PT
42. l power of the solution hook up PEAKS Online to PEAKS Client for batch submission of jobs and preprocessing from RAW data How to use this user s manual This user s manual is intended to help us get started using PEAKS Online 2 0 acquaint us with its functionality show us how to customize PEAKS Online to our application allow us to work efficiently with the interface provide a task based reference and help us with troubleshooting As such this manual is organized into chapters based on these categories Use the table of contents at the front of this manual to access the relevant section Step by step instructions for some tasks can be found at the end of the respective chapter Click the respective icon in the left hand border to navigate to that section for directions What is PEAKS Online To use PEAKS Online after an account has been created fill out the necessary fields that are present in the data submission form The data selected for uploading will be processed by the internal network s cluster The size of the data file will determine how much time will be required for the submission to complete If the data is on the local network and the network is fast the submission will proceed quickly With a gigabit network running at full capacity 1 GB of data can be transferred to the cluster in 8 seconds With a 100Mbit network the same amount of data would be transferred in 80 seconds Alternatively if the file is being moved acro
43. lutions to difficult otherwise unsolved problems that have resulted in research bottlenecks At BSI we are not satisfied with a solution that goes only partway to solving these problems our solutions must offer something more than existing software The BSI team recognizes that real people will use our software tools As such we hold in principle that it is not enough to develop solely on theory we must develop with customer needs in mind We believe the only solution is one that incorporates quality and timely results a satisfying product experience customer support and two way communication So then we value market research development flexibility and company wide collaboration evolving our offerings to match the market user s needs Efficient and concentrated research development customer focus and market analysis have produced PEAKS software for protein and peptide identification from tandem mass spectrometry data RAPTOR and PROSPECT Pro software for threading based 3D protein structure prediction and PatternHunter software for all types of homology search sequence comparison 56 PEAKS Online Terms of Service HIS PRODUCT AND RELATED SERVICES ARE PROVIDED SUBJECT TO THESE TERMS AND CONDITIONS PLEASE READ THE FOLLOWING INFORMATION CAREFULLY YOUR CONTINUED USE OF THIS SITE WILL INDICATE YOUR AGREEMENT TO BE BOUND BY THE TERMS AND CONDITIONS SET FORTH BELOW IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS PROMPTLY EXIT THI
44. matic experimental error is on the patent precursor ion that PEAKS will account for in its analysis A user will type a number in the textbox to represent this Select the units PPM or Daltons from the dropdown list The best choice for the error is generally dependent on your instrument type Fragment tol Fragment Tolerance is the peak matching error tolerance to be used when analyzing the fragment ion spectrum It determines how much random and systematic experimental error on the fragment daughter ion PEAKS will account for in its analysis Users can type a number in the textbox and also specify units Precursor mass The mass of the precursor ion can be set either as a monoisotopic mass of as an average For ion trap instruments it is sometimes beneficial to allow the PEAKS Protein ID database search to use an average mass Choose the database Only one database can be chosen per analysis Locate the desired database using the dropdown list 27 Jump to the Assistance section to use the Taxonomy tree Selected taxonomy This field is only applicable if the NCBI nt or Swiss Prot database has been selected in the Choose the Database field This will help narrow the search to the taxonomy of choice and limit your results by the same measure Taxonomy tree If the Database to search has been configured for taxon based searching this list will allow us to select limit which taxa ate searched
45. minus Add Update enzyme Remove selected enzyme 33 Enzyme list PEAKS Online has a number of enzymes that come prepared for immediate use These can be found in the Enzyme list There are many more enzymes that exist and a user may be interested in using during their PEAKS Online analysis Therefore the administrator has the ability to add new enzymes to the list PTM configuration Jump tothe PEAKS Online has a number of post translational modifications that come prepared for DEN immediate use These can be found in the PTM list There ate many more PTMs that exist add update 2Md a user may be interested in using during their PEAKS Online analysis Therefore the or remove administrator has the ability to add new PTMs to the list PTM PTM list PEAKS Online has a number of PTMs that come prepared for immediate use These can be found in the PTM list There are many more PTMs that exist and a user may be interested in using during their PEAKS Online analysis Therefore the administrator has the ability to add new PTMs to the list PTM configuration PTM list PTM info rnospnopantermemne A Name Phosphorylation Palmitoylation Abbreviation Phospho Biotinyl iodoacetamidyl 3 6 dioxaoctanediamine Mass 79 966331 Neutral loss 0 0 Phosphorylation O Residues that can be modified O phosphorylation 5 T Everywhere STYHCD N terminus Acrylamide adduct C terminu
46. n those resources explicitly to the proper groups 13 When all configurations are complete users may start using PEAKS Online 15 Account Pane he purpose of the Account pane is to display registered user information For any reason this information can be modified updated by the group administrator s Create an account Jumpto For users evaluating PEAKS Online an account will be submitting and processing jobs Losing via the BSI cluster This will mean that a User will not need to install any software onto this chapter his her own computer or cluster Thus effectively the User will be his her own account for administrator A new User will need to create an account in order to provide the BSI instructions to create an evaluation account Results Search Settings Admin GroupAdmin Monitor Login email aperson bioinfor com Full name Ahuman Person Organization name Bioinformatics Solutions Inc Change password did For users with full version privileges an account will be created for you on behalf of an ump to 03 x d rie administrator The administrator will be a key resource for adding and removing certain Assistance features within PEAKS Online 16 Jump to the Assistance section to change a password Forgot password In the event that an account owner forgets his her password the password can be sent automatically to the registered PEAKS Online login email address Login em
47. nnection with a normal peer reviewed scientific publication or presentation or the like of the results of your life science research experiments You must acknowledge your use of the Analysis Center in any such publication or presentation according to academic tradition You may post the results of your queries to or downloads from the PEAKS Online in connection with posting the results of your life science research experiments on a non commercial not for profit Web site You may not post any results or downloads from the Analysis Center or any other content from the Site on a commercial or not for profit Web site Evaluating users only Trademarks BSI logos look and feel branding catchphrases trademarks and service marks may not be used in connection with any product or service that is not BSI s in any manner that is likely to cause confusion among customers or in any manner that disparages or discredits BSI Our Use of Evaluator Data and Communications BSI will maintain security procedures with respect to its access and maintenance of the Data including protein or nucleic acid sequences and mass spectrometry data evaluators submit in queries to the BSI public cluster via PEAKS Online which provides reasonably appropriate technical and organizational safeguards against unauthorized disclosure or access consistent with the following By using the evaluation Site you authorize and hereby grant BSI a limited non exclusive royalty f
48. number of organisms GroupAdmin Pane Assistance This section will lead users through step by step instructions which should be followed to maximize ease through the PEAKS Online software Database configuration New database To configure NR or Swiss Prot databases SA OS D ES A user will need to check this box to enable editing properties Once the name path taxid taxdmp fields are entered Click apply button to save the changes To change the configuration simply edit the fields Click apply to make the change take effect For customer databases to set a new database Qvi da c9 IUE Click on the New db button Give the database a name Direct PEAKS Online to where the database can be accessed either manually Select the database format using the drop down menu If this is an EST database click the box to the left Once configured click Add Update Database to add it to the list of useable databases To change the configuration of an existing database 1 2 3 4 Click on the database name in the database list The database s properties will be shown on the left Change the properties to the new value Click add update database to make the change take effect 50 Remove selected database To remove a database Click the box beside the undesired database in the Database list Press Remove selected Database O It will be removed from PEAKS Online As this will no
49. oad Browse Swiss Prot Public Format Swiss Prot IPLHUMAN Public This is an EST database IPLMOUSE Public v Add Update Database Remove selected Database Enzyme configuration u PTM configuration Select a group As a group administrator one can set participant permissions This dropdown list shows all the groups that the login user is the group admin Select the group the user want to manage Jump to the Database configuration New database Assistance section to configure or PEAKS Online requires a protein or EST database in FASTA format to identify protein addanew candidates Since databases are constantly being updated and each group may have their own database database preference PEAKS Online does not provide a protein or EST database Thus it A will need to be download from the Internet and PEAKS to be informed where the database database 48 Jump to the Assistance section to add a new enzyme update an enzyme remove an enzyme Jump to the Assistance to add a new PTM update a PTM remove a PTM is located PEAKS provides the Database configuration as a tool to easily set this up Also from here we can edit a database s properties load a new database or remove an existing database PEAKS Client uses the databases configured on the PEAKS Online server Database list This is a complete list of databases available to this group
50. ree perpetual world wide irrevocable license to reproduce transmit display disclose and otherwise use your Data solely for the purposes of processing your requests and transactions maintaining and improving the Site but not for exploiting your Biological Data for other commercial purposes unless otherwise provided in a separate written agreement you may have with BSI Evaluating users only YOU ACKNOWLEDGE THAT SECURITY SAFEGUARDS BY THEIR NATURE ARE CAPABLE OF CIRCUMVENTION AND BSI DOES NOT AND CAN NOT GUARANTEE THAT DATA OR OTHER INFORMATION CAN NOT BE ACCESSED BY UNAUTHORIZED PERSONS CAPABLE OF OVERCOMING SUCH SAFEGUARDS IN PARTICULAR THE SITE MAY BE USED TO ACCESS AND TRANSFER INFORMATION INCLUDING DATA OVER THE INTERNET YOU ACKNOWLEDGE AND AGREE THAT BSI DOES NOT OPERATE OR CONTROL 58 THE INTERNET AND THAT D VIRUSES WORMS TROJAN HORSES OR OTHER UNDESIRABLE DATA OR SOFTWARE OR I UNAUTHORIZED USERS eg HACKERS MAY ATTEMPT TO OBTAIN ACCESS TO AND DAMAGE THE SITE AND OR YOUR BIOLOGICAL DATA AND OR OTHER INFORMATION COMPUTERS AND OR NETWORKS BSI SHALL NOT BE RESPONSIBLE FOR SUCH ACTIVITIES YOU ARE SOLELY RESPONSIBLE FOR THE SECURITY AND INTEGRITY OF YOUR INFORMATION AND SYSTEMS Acceptable Use You must not transmit any data or material on or through the resource that a constitutes or encourages criminal conduct gives rise to civil liability or otherwise violates any law b violates or infringes the right
51. s Middle only m Pyridoxal phosphate Rule Cisin only Prokaryotes S carbamoylmethylcysteine cyclization N terminus eS ji E Updat Remove selected PTM ES 34 Jump to the Assistance section to add a new user User management User management is a tool to help the administrator to create edit and remove a user s profile The user list on the right shows all user accounts in the PEAKS Online system The information on the left shows the account details of a particular user The member of section in the middle shows which groups the selected user belongs to User list 228 user s User Info pa ote rau AAA TE Login email jninshou facelife org El Ahuman Person aPerson bioinfor com z Password eecccccceccce Confirm 9999999929 O Brian Persoon bPersoon company com cns ERE Full name Jennifer Ninshou O Christina Personne cPersonne university edu Organization Bioinformatics Solutions Inc O Donna Menschlich dMenschlich pharma com z e Disable Force change password at next login O Edward Tp owno Edward biotechcamp com d d sep g Member of O Frankie Persona Frankie colleycross com Y Administrator A O Gordon Pessoa gPessoa proteinstudy com bPersoon company com E O Henry Mepcona HPPApuli net O gPessoa amp proteinstudy com F P ES P J O Ira Ren iRen SMIS ca O kYin more research edu O Jennifer Ninshou jninshou amp bioinfor com O mStanford msmsresearch uk
52. s done Installing JBoss done Configuring PeaksOnline done Deleting temporary files done PeaksOnline Server has been successfully installed 6 Go back to the Portal server main server in the command line change to the target directory and run command java jar polupdate jar jboss default Note if it is an All in One installation use the below command instead and go to Step 8 java jar polupdate jar jboss all 7 On all cluster nodes in the command line change to the target directory and run command java jar polupdate jar jboss all 8 On the cluster master node run start_pol bat or start_pol sh under d peaksonline test jboss bin directory to start the master node Wait for about 2 minutes until the master node is fully loaded run start_pol bat or start_pol sh on each cluster slave node 9 On the Portal Server main server run start_pol bat or start_pol sh under d peaksonline test jboss bin to start the portal Wait for about 1 minute until the portal server is fully loaded 10 Open a web browser Internet Explorer is recommended and type in the address http your_portal_server 8080 peaksonline register jsp 14 In the page please fill out the information and click register If you see the login page the registration is successfully complete If not this means the Portal Server is having difficulty connecting to the BSI licensing server In this case go to d peaksonline test jboss server def
53. s The amount of disk space required for result files depends on how long the customer wants their result to be on line and on the overall search profile File sizes of individual result files range from several KB to hundreds of MB MYSQL database data file MYSQL data files are relatively small and increase in size very slowly over time Uploaded data files These files are basically what users uploaded to PEAKS Online server The system admin may delete these files periodically to save disk space Since hard drives ate quite inexpensive we recommend a large storage space An SATA or SCSI drive with more than 200GB is appropriate for an all in one installation or for the main node of a cluster Processing nodes in a cluster require only a few hundred megabytes of disk space Operating system PEAKS Online is built on the powerful and robust Java Enterprise technology So theoretically it can run on any operating system Sun Java supports Here is the link to the supported system configurations We have not tested PEAKS Online on all the platforms but below are the operating systems we have tested Windows Vista Windows XP Professional Windows Server 2003 Fedora Core 4 Fedora Cote 5 Solaris 10 SUSE Linux Debian GNU Linux Pre installation Instructions The IT rep must prepare the server before PEAKS Online can be installed The following steps must be completed Hint if you paste the result of each step
54. s of any third party including without limitation patent copyright trademark privacy or any other proprietary right or c contains a virus or other harmful component BSI reserves the right at all times to disclose any information as necessaty to satisfy any law regulation government request court order subpoena or other legal process or to edit or remove any information in whole or in part that in BSI sole discretion is objectionable disruptive to the resource or in violation of these Terms and Conditions Accuracy and Integrity of Results Although BSI attempts to ensure the integrity and accuracy of results provided by PEAKS Online BSI makes no guarantees or warrantees whatsoever as to their correctness or accuracy In the event that an inaccuracy arises please inform BSI so that it can be corrected No Warranty THE RESOURCE ANALYSIS CENTER AND ALL INFORMATION AVAILABLE THROUGH THE RESOURCE ARE PROVIDED AS IS WITH ALL FAULTS AND AS AVAILABLE BSI DOES NOT WARRANT THAT THE SITE WILL MEET YOUR REQUIREMENTS OR THAT THE RESULTS OF ANY QUERY WILL BE COMPLETE OR ACCURATE BSI DOES NOT WARRANT THAT ACCESS TO THE SITE WILL BE UNINTERRUPTED OR ERROR FREE OR THAT DEFECTS IN THE SITE WILL BE CORRECTED WITHOUT LIMITING THE FOREGOING BSI DOES NOT REPRESENT OR ENDORSE THE ACCURACY OR RELIABILITY OF ANY SEQUENCE DATA ANNOTATION DESCRIPTION IDENTIFICATION OR OTHER INFORMATION DISPLAYED DISTRIBUTED HYPERLINKED OR OTHERWISE REFE
55. ss the Internet the time for submission will depend on the speed of your Internet connection The actual processing time of the data will depend on the number of PEAKS Online nodes in the cluster With PEAKS Online 2 0 not only will a notification email will be sent to the user s email account but also the results can be found in the user s search history located in the Result pane Submitted input will appear in the email for reference including a time stamp of when the job was started and finished If difficulties are experienced with submitting or receiving the results please contact the PEAKS Online Administrator Customization There are two levels for customization The PEAKS Online administrator is responsible for the configuration of global and public resources This person is also responsible for the privilege settings etc The other level of customization is under the group admin role A group admin can define the private databases enzymes and PTMs for a particular group and by default only the users in this group can access those private resources New private or public databases can be added to the databases dropdown menu listing Enzymes and new PTMs post translational modifications can also be added to the interface A User can define PTMs variable or fixed for a particular job but these will need to be re keyed to use them for later use Getting started with PEAKS Online 2 0 Everything we need to know from the beginning and
56. stall the slave node for the cluster installation Installation type choose 1 to 5 2 Please specify the amount of memory PEAKS Online may use 2000 Please specify how many CPUs Cotes are in this server 2 Delete old peaks database in MYSQL yes no yes License agreement Do you accept the license agreement to install the product yes no yes Extracting PeaksOnline components done Installing JBoss done Configuring PeaksOnline done Deleting temporary files done PeaksOnline Server has been successfully installed 4 On the cluster master node in command line change to the target directory and run the command java jar polinstaller jar install config A screen shot can be seen below in grey Note Choose 4 Cluster master as the installation type D peaksonline test gt java jar polinstaller jar install config Please choose the installation type 1 All in One Install all components in one server 2 Portal server Install the portal server for multi server installation 3 Process server Install the process server for two server installation 4 Cluster master Install the master node for the cluster installation 5 Cluster slave Install the slave node for the cluster installation Installation type choose 1 to 5 4 Cluster nodes 0 192 168 1 100 1 192 168 1 101 2 192 168 1 102 Please choose the address for this server 0 2 1 Please specify the amount of memory PEAKS Online may use
57. t permanently remove or delete the database the database will be able to be used again in the future if it is re entered into the Database list using the standard database configuration instructions Enzyme configuration New enzyme Note Built in To create a new Enzyme enzymes can not be modified e Click the New enzyme button Give the Enzyme a name one that easily explains its form function Enter the Digestion rules that correspond in the following boxes o The text boxes on the left are for residues at the end of a peptide the boxes on the right for those at the start of a new peptide Use set brackets around he residue to denote any amino acid except the ones enclosed in these brackets O The letter X can be used to denote any residue Further a user can specify a more particular preference for handling this enzyme simply by clicking on button of their preferred choice O Find peptides that satisfy the above at both ends O Find peptides that satisfy the above only at C terminus and or peptides that satisfy the above only at N terminus e Once each setting has been entered click Add Update enzyme to add it to the Enzyme list 51 Note Built in PTM can not be modified Update enzyme To Update or modify an existing enzyme Click the particular enzyme in the Enzyme list O The name will appear in the Name text box as well as the Digestion rules will appear Modify the N
58. ticular group can be done by selecting the box beside the group s name in the Group list selecting the box beside the particular enzyme name in the Group enzyme section pressing the Add Update group button O As with other sections a Select all and Deselect all option is available for administrative convenience Group PTM To assign a PTM to a particular group e Select the box beside the group s name in the Group list e Select the box beside the particular PTM name in the Group PTM section Press Add Update group O As with other sections a Select all and Deselect all option is available for administrative convenience Group options To allow account search submission and or result retrieval privileges e check the appropriate box To restrict this privilege leave this box unmarked Mail server require authorization Check this box if the mail server requires a user name and a password to send email If not leave it unmarked 47 GroupAdmin Pane he GroupAdmin pane allows a representative of an particular group to configure such things as databases enzymes and post translational modifications Account Results Search Settings EE GroupAdmin BRU Gis Select a group aPerson amp bioinfor co Y Database configuration a Database list Database info C Pharma 138 Name Pharma 138 O csr octe Path usr jboss 4 0 35P1 server default pol data root custon NCBI nr Public Upl
59. to be reported Time zone When PEAKS Online produces an output file it will make a time stamp so any person viewing a report can be confident when the result was produced Admin email BSI Bioinformatics Solutions Inc makers of PEAKS Online are constantly improving the software and will use the provided Admin email address to inform the organization of upgrades This email address will appear in the sender s line of all emails sent from PEAKS Online Mail server hostname A mail server hostname is the unique name by which a network attached mail device is known on a network The hostname is used to identify a particular host in various forms of electronic communication such as e mail Enter the organization s mail server hostname domain name or IP address of the SMTP email server in this field Mail server port The port number which the email server is listening The default standard port is 25 Mail server user password This category can be used to block certain domain names and simply maintain higher security in favour of the Administrative organization 39 Log file The log file keeps a written record of PEAKS Online s actions It is highly effective in recording information used for bug tracking The PEAKS Online Administrator will set the location of the log file users can not change it 40 An EST database is a division of the GenBank that contains sequence data and other information on single pass cD
60. ue Select the box that corresponds to the desired file O Multiple files may also be removed by selecting multiple boxes Press Remove selected searches Once a search enters the running status it can no longer be removed 21 Search Pane hen a user is ready to start processing data they will need to enter certain parameters for optimal results The Search pane is designed to be very straight forward and extremely efficient in terms of collecting the vital information Account Results Select a group Search title Enzyme Modification User defined PTM Function Preprocess Merge tol Instrument Parent tol Fragment tol Precursor mass Settings japerson bioinfor c Y Admin Available modifications One C aB_old_ICATdO 148 old 1CATds Cl ICAT light Cl ICAT_heavy Fixed Variable O Find de novo sequences 9 PEAKS Protein ID O Use existing de novo results v Do preprocess O Enable filter o Da M 9 Monoisotopic O Average GroupAdmin Monitor Data file Allow up to 3_ missed cleavages Selected modifications Set fixed gt lt Unset PTMs Allow up to 3 variable PTMs per peptide Choose the database Swiss Prot ot_sprot Selected Taxonomy Taxonomy tree No taxa have been se You may focus your search bys g taxa fromthe Taxonomy Tree ifthe databas nfigured for it Identify PTMs in known proteins Subm
61. up will have the checkbox checked 2 Group administrators All users who can manage the selected group will have the checkbox checked 3 Group databases All the databases available to the selected group will have the checkbox checked 4 Group enzymes All the enzymes available to the selected group will have the checkbox checked 5 Group PTMs All the PTMs available to the selected group will have the checkbox checked 6 Group options All user permissions 7 Misc group settings Technical set up of the PEAKS Online system including mail server configurations Group name This is the name of the currently ae databases selected group roup enzymes Select all Deselect all argc Built In Group fields Maspn Built In Asp N N terminal Glu Built In The section on the far right within Group management provides such V chymotrypsin Group topics and details as databases Wenger Built In enzymes PTMs and options ENDOZYME wyangUDbioinfc Group databases displays all Y aluc bicarbonate Built In databases available to each group Glu C phosphate iss Group enzymes displays all enzymes MLysC Built In available to each group Mns Built In Group PTMs displays all PIMs M Pepsin pH 1 3 Built In available to each group Pepsin pH gt 2 Built In Group options provides access to Proteinase K Built In v lt Group PTMs maintain a steady flow of research Group options between groups to share the cl
62. uster Such features to be used include allowing search submission allowing result retrieval maximum number of searches per day maximum file size in Megabytes maximum number of spectrum total customer db size in Megabytes Misc settings The Misc Miscellaneous section is responsible for the truly technical side of PEAKS Online The applications provided include Disable Security Data file directory s Z Report Top e Time zone Admin email Mail server hostname Mail server port Mail server require authorization Mail server user name Mail server user password Blocked email domain for sign up Log file f Misc settings Disable security a Data file directory usr jboss 4 0 35P1 server default pol data root Report Top 5 Time zone EST Sd Admin email aPerson bioinfor com Mail server hostname 19216812 i o m Mail server port 5 y Mail server require authorization Mail server user name poladmin Mail server user password PeaksOline K Apply changes Help 38 Disable Security Currently PEAKS Online security can not be disabled Data file directory The Data file directory is the root location where all produced data files will be stored upon complete processing The files stored here include uploaded data files result files uploaded customer databases etc Report Top The number of top candidates
63. y applicable end user license agreements Except as provided in these Terms and Conditions any use of these materials on any other Web site for any purpose is prohibited Ownership The PEAKS Online software is a proprietary product of BSI and is protected by copyright laws and international copyright treaties as well as other intellectual property laws and treaties BSI shall at all times own all right title and interest in and to the Software including all intellectual 57 property rights therein You shall not remove any copyright notice or other proprietary or restrictive notice or legend contained or included in the Software Any link to this resource must clearly identify BSI as the creator of PEAKS Online BSI reserves the right to redirect any links to the Site to any page it chooses Evaluator Submission of Data and Use of Results Evaluators of PEAKS Online may not use any software robot or any web form for submission of data including but not limited to Mass Spectrometry data files sequences databases enzyme and post translational modification definitions to PEAKS Online except those web forms and software provided by BSI You may not use PEAKS Online or results from PEAKS Online within a commercial or for profit software application or otherwise charge for access to or use of any such results or content from the Site without BSI s prior written permission You may publish the results of your queries to PEAKS Online in co
64. zyme CONPIQUTANON e 33 Enzyme list PTM configuration User ManQgeMENt m hd ro M Group management MI e O Y Group fieldss voe b E bti uas Lb UU D LE UEM Misc settings Admin Pane Assistance DGtabaSe CONSULTA ir A A A A a Eos 41 New database 41 Customer database 41 Remove selected database 42 Enzyme Conf oura ON T 42 New enzy ME ssar eNe E E EE EEN EEEO E EEEE EERE ERRORE pd ride Update enzyme Remove selected AMI MN A AA 43 PIM CONIPUFatiOn ues edu E Et IR MN pet M CE MM ld MEUM MAD MAU E 43 New PTM 43 Update PTM 44 Remove Selected PTM 44 US EMANAN SE Adda dset uoc DO MEME M MM M M M E Disable user access Force password chan e 45 Update SCR tet otal a E Remove user Group TANG ZEMEN usas CIS RAR AA ARA A Sa sac SEE aa id P eee p Euh e Aeneas 46 Group Us ira M 46 Add Update group 46 Remove selected group 46 Group database 46 Group ENZYME ios lia 47 GTOUP PEM m n 47 Group OP td OMS ri ETE 47 GROUPADMIN PAN

PEAKS Online Manual 2.0

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