User Manual - ForensicDB.org
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1. the JCAMP file can be saved in a user s local libraries Spectrum Meta Data Pane The Spectrum Meta Data pane provides information on the instrumental parameters used to collect the spectrum located in the Spectrum pane Within one record there may be multiple spectra documents thus there may be several Spectrum Meta Data panes within one record Figure 12 Spectrum Meta Data spectral method El MS scan range 40 600 Mass calibration method PFTBA single compound or mixture single compound Gas type He Notes 70 eV lonization mode positive Wass measurement nominal Instrument type quadrupole Chromatography type GC Tune type auto tune Instrument make and model Agilent 5973 Method and software used in data processing averaged and background subtracted Chromatographic method Column R amp 5MS 30 m x 0 32 mm x 0 5 um Split ratio 15 1 Injection port temperature 300 C Temperature ramp 240 C hold 1 min to 300 C at 30 C min hold 27 min Figure 12 Spectrum Meta Data pane 10 ForensicDB A Web Accessible Spectral Database Structure Pane The Structure pane shows the structure of the compound that gives rise to the spectra found in the Spectrum pane To export a structure as a MOL or other file format e Select the Export icon There are three main search related tools provided in the Structure pane which can be accessed by right clicking within the Structure pane Figure 13 Search Cur2. 158 00004 Search Spectrum Similar to Current Set Record as Reference WE s 220 0 114 00004 Set Reference Spectrum for MASS Clear Reference Spectrum for MASS 250 300 350 mz Figure 10 Spectrum view options 50 100 150 200 As outlined in Figure 10 there are many tools for changing the view of the files shown in the Spectrum pane or accessing other options These options can be found after right clicking within the Spectrum pane Zoom in on the spectrum by left clicking and dragging over the peak of interest Zoom out by right clicking within the Spectrum pane and selecting Zoom Out Enlarge the spectrum by selecting Open in Window or double left click on the spectrum Select Search Spectrum Similar to Current to find spectra similar to current spectrum in database This is a similarity search for a spectrum already within ForensicDB to find other similar spectra in ForensicDB ForensicDB A Web Accessible Spectral Database e Select Set Reference Spectrum for MASS to show the current spectrum mirrored to all other spectra To return to normal view select Clear Reference Spectrum for Mass Some records have multiple spectra Users can navigate between the spectra using the green arrows located at the top of the Spectrum pane Figure 11 Spectrum MASS aen Figure 11 Navigating between spectra within a record To export a spectrum as a JCAMP file e Select the Export icon in the Spectrum pane e Once created
3. Cope cid RM UOS taht 17 Drawias applet date 17 User BEEN is Tt 18 SO e eio ibo ER A uve tedio taata eus 19 Saye scheme didlo DO iii 19 TAE VIEW AAA 20 Select CO UITIBS dece laden ias 20 Select datadosshow 1n tne CODI A 2 CN 21 CHOOSE TE POr OMA as 27 Select atenmis to include ING TEPOM io 22 INOGfIcatiomorecreated JCA VIP Tesien 24 bao DC uri E 29 Search similar Spectra SeLULDIPS pepini E A Ioab idt 26 Number of records OU varas 26 Summary Aea SEE en EA EEE E E E E 2 Select data type fO SUDNI orea id 28 Enter Ete cord nto rm ODD dco cette udo a do 28 Enterainstrumental parameters odora do 29 Notitication of submitted dati asada 29 iii ForensicDB A Web Accessible Spectral Database 1 Introduction to ForensicDB The intent of this User s Manual is to provide information to the reader on accessing navigating and searching ForensicDB www forensicdb org ForensicDB is a free community driven peer reviewed and Web accessible database of multiple spectral methods including nominal mass accurate mass and FTIR data The database is searchable by spectrum structure calculated properties and submitted information such as compound name The goal of ForensicDB is to provide the forensics community with reference spectra to aid in the identification of unknown compounds RTI International RTI has worked to include many of the emerging designer drug compounds and will continue to populate ForensicDB with data of forensic inter
4. Figure 16 Explore Af Database Search Records Figure 16 Search Records tab This will open the Main Search Form Figure 17 En x A 4 Search gf Clear Forms Main Search Form E Multiple Database Search C Perform search in List A records only Spectrum Search Spectrum Similarity Search Spectrum Parameters User Data aja Bl E Figure 17 Main Search Form Conducting a Basic Search You can conduct two types of basic searches on the Main Search Form e Search by Formula Weight Type a specific number or a range by placing two decimal places between the range 303 304 e Search a Formula Make sure there is a space between each symbol C24 H23 N O Within the Main Search Form there are three options that are selected that lets the system know what to search e The Current Database Search option lets the system know that all searching will be done in the current database This option 1s automatically selected as default and should remain selected as there 1s only one database within ForensicDB 13 ForensicDB A Web Accessible Spectral Database e The Perform search in all records option is selected as a default option and lets the system know that searches should be completed on all possible records within the database e The Perform Search in List A records only option is a specialized search option that is used to narrow down a set of returned results from a previous sea
5. with the averaged retention times and the x and y axis information Figure 32 24 ForensicDB A Web Accessible Spectral Database a 02201204 D Average of 29 776 to 29 853 min jdx Notepad File Edit Format View Help KSTITLE Average of 29 726 to 29 853 min jdx SEJCAMPDX 4 24 DATA TYPE Mass Spectrum NPOINTS 349 SEXYDATA XY XY 41 1 11840 42 1 634 44 1 18798 45 1 355 45 9 10 46 0 11 46 2 30 49 1 34 30 1 913 31 1 2652 32 1 566 33 1 817 34 1 240 35 1 2135 36 2 986 37 2 7661 38 2 358 38 9 17 39 2 36 61 0 104 62 1 1166 63 1 3075 63 9 31 0 Figure 32 View of JCAMP file Directions for searching ForensicDB directly from Agilent ChemStation Select OK in Figure 31 if you have Internet access at the instrument computer and want to search similar spectra 1n ForensicDB A Search Similar Spectra dialog box is shown Figure 33 This will allow you to adjust search settings and it is similar to that described in Section 5 Figure 19 e Searching through Agilent ChemStation software is different than searching through the ForensicDB interface in that only a maximum of 9 resulting spectra will be returned e Creating a mirrored reference of your searched spectrum is not a feature when searching through Agilent ChemStation 25 ForensicDB A Web Accessible Spectral Database 4 Search Similar Spectra ioj x Include M lon v Use Minimal Similarity 5 Figure 33 Search Similar Spectra se
6. ForensicDB A Web accessible Spectral Database ForensicDB A Web Accessible Spectral Database Table of Contents Introduce onto Ernie SOo a l y 26 1 S EO DB aaa E do A caos I SELL SNS tem PT OPEL CS xan cccey oteicatet avetncrntanace Mmm MM M FPEM PEL MI MR PAM IDE 5 Spec Properties ai e ree 9 Pranie Y cuestan catu A RN UE 6 p AN ANA AUIS Me Database ra a Eco 7 Navicanon mi oro eet 7 Using the Default Database Home Page amina aiii 8 Si A O 13 Conductinea Basic Cd da 13 Conductine a Spectrum similarity Serra 15 Cond etiune d Structure Search ica 17 Conductins a Search Of User Dita A A AAA DA AO 18 Savi Search CLIN ld ia 19 REVIEWING Rest aia iia 20 Navigating search results using table VIE W oooccccccccnonononcnnnnnnnnnonononnnnnnncnnnonnnnnnccnnnnnnnnnnos 20 Set up the columns to view information of interest nnne 20 Creatine a Report OT Search Resulta o cd 21 s Ad OEE AUCs is 23 Conducting a ForensicDB Spectrum Similarity search from Agilent Chemstation 23 l sta on regu reni is nesr ose ation esse A an 23 Creating a JCAMP file from Agilent ChemStation eese 24 Directions for searching ForensicDB directly from Agilent ChemStation 25 Submituns Spectra to Forensic DB 255i eto bao EE nicl mater bead Dune Lo tua id 28 Contact Into Hr da dacal ecm ialeeieecew 30 List of Figures Fig re L POrensic DBD AC6CeSS Dae 6 vaselina 2 LFisuie 2 PorensicDB LEo9upaBesns pi
7. Settings diskette at the top of the Main Search Form Figure 23 For example you can save a User Data search for submitted name or instrumental parameter so that it 1s easily set up for subsequent searches eo Explore j V Database 4 Search Records Xa e Search Queries 18 En a d Search gf Clear Forms Figure 23 Save search settings A Save Scheme dialog box will appear Enter a name to save the scheme Figure 24 Save Scheme Webpage Dialog Save This Scheme As Spectral method search e OK X Cancel Figure 24 Save scheme dialog box To access those saved settings select the dropdown menu within the Search Queries which is located to the right of the Save Settings diskette in Figure 23 19 ForensicDB A Web Accessible Spectral Database 6 Reviewing Results Navigating search results using table view There are several ways to view data within ForensicDB These are by One Record View Tile View and Table View The One Record View is shown in Figure 9 You will only be able to view one record at a time The Tile View option shows a table of all structures within the database The Table View option can make the viewing of search results easier and more customizable Directions for accessing the Table View are described below e Within the Database tab click the Change DB view icon and choose Table View Figure 25 One Record View H Hle View EH Table View Figure 25 Table view e Right cli
8. ass Cannabimimetic Submitter email custservig caymanchem com Figure 14 Record Data pane Molecule User Data Pane The Molecule User Data pane shows information calculated from the structure Figure 15 Such information includes the monoisotopic mass average mass and molecular formula Molecule User Data Formula Era HO FW 385 4981 InChl InChl21 C265H27N02 c1 4 5 10 17 27 18 2 25 22 13 8 8 14 23 22 2 7 26 28 21 15 16 24 29 3 20 12 7 6 11 18 20 21 h6 8 11 16H 4 5 10 17H2 1 3H3 SMILES COc2ccc c1ccccc12 0 0 cAc3ccccc3n CC CCC cAC InChl Key CHTCHEBQGOGFICNE LUHFFFAOYAS Molar Refractivity 117 8120 5 cm Molar Volume 348 8 7 0 cm Parachor 875 448 0 cm Index of Refraction 1 590 0 05 Surface Tension 39 6 7 0 dyne cm Density 1 10 0 1 g cm Dielectric Constant cannot calculate Polarizability 46 70 0 5 10 cm Monoisotopic Mass 385 204179 Da Mominal Mass 385 Da Average Mass 385 4981 Da M 385 203631 Da M 385 204728 Da IM H 386 211456 Da M H 386 212553 Da M H 384 195805 Da M H 384 196903 Da pKa The structure does not contain ionization centers calculated by current version of amp CD pka Figure 15 Molecule User Data pane 12 ForensicDB A Web Accessible Spectral Database 5 Searching the Database To search the database switch from the Database tab that shows the default Database Home page to the Search Records tab in the menu at the top left of the page
9. ate mass data on mass spectra The Frame properties are used to set the spectral setting so that you can see all spectral data such as mass FTIR and chromatographic data Spectrum Properties To set your Spectrum properties e Select the Settings icon located at the top of the default Database Home page on the right This will pull open the Settings Dialog page Figure 6 e On this page click the Spectral Display option found on the left sidebar This will open the Spectra Display Template e Set the Data Type field to MASS and the Template field to MASS TPT e Then click OK ig Settings Webpage Dialog ea Spectra Display Templates structure Display Data Type MASS i Template MASS TPT Spectral Display Structure Search FE Spectra Similarity e Multiplet Search e OK X Cancel Figure 6 Settings for accurate mass on the Spectra Display Template Once you click OK you will be taken back to the default Database Home page ForensicDB A Web Accessible Spectral Database Frame Properties Now it is time to establish your spectral view settings e To display and navigate between mass FTIR and chromatographic data on the default Database Home page select the Database tab located at the middle tab on the upper left menu options E a e Select the Properties icon a in the Spectrum pane This will open the Frame Properties page Figure 7 e On this page clear the Analytical Data Type bo
10. ccessible Spectral Database 7 Additional Features Conducting a ForensicDB Spectrum Similarity search from Agilent ChemStation Additional functionality has been introduced to facilitate spectrum similarity searches on ForensicDB using Agilent ChemStation files Both of these files are available at www forensicdb org This functionality was added with two purposes in mind 1 Allow users to search an unknown spectrum directly from Agilent ChemStation eliminating the extra steps described in Section 5 Conducting a Spectrum Similarity Search a This requires that an Internet connection and Internet Explorer 6 0 or greater be installed on the instrument computer 2 Create a JCAMP file that can then be searched in ForensicDB as described in Section 5 Conducting a Spectrum Similarity Search a Mass spectra from Agilent ChemStation software are exported as CSV files These CSV files are not acceptable file formats to be uploaded into the Spectrum Similarity search within ForensicDB Figure 18 Section 5 In order to resolve this issue we have worked with an outside consultant to create Agilent ChemStation macros that will export mass spectra as JCAMP file formats that can be uploaded to search within ForensicDB b This does not require an Internet connection on the instrument computer Users can transport the created JCAMP file to a secondary computer with an Internet connection Installation requirements Installation Disclaimer Use
11. ck within the table and click the Select Columns option Figure 26 One Record View FH Tile View dl Hide Column sve Setup Columns Select Columns E3 Save Setup Sel save Common Setup Figure 26 Select columns Set up the columns to view information of interest Y ou can set up the columns to view information of interest For example Figure 27 presents the column set up to show submitted name structure submitter facility standard source spectral method and MS similarity e If working with several different table view settings use the Save Settings option similar to that described in Conducting a Search of User Data section 5 to save a table view for later use e Double left click within the table view or select One Record View Figure 25 to return to viewing only one record at a time 20 ForensicDB A Web Accessible Spectral Database E Select Columns Webpage Dialog Invisible Data Selected Data Submitted Name amp ID E j Structure FPLATE SIZE Submitter facility Acquisition date a 4 Standard source ChemSpider Spectrum Spectral method Class pee Spectrum MS Similarity Collaborator Collaboratorlomments CollaboratorDecision CuratorComments Data Type Data GC Data MASS Row Height 100 w OK X Cancel Figure 27 Select data to show in the columns Creating a Report of Search Results T
12. compound name For easy access to compound information and links to database records SMILES and INCHI information see our J V H compound and cathinone quick reference guide About us Help Contributors Forensicdb org is a publicly available cheminformatics data library providing the ability to search a given spectra against a Web Contact Us accessible database of reviewed spectra and have spectra from multiple spectral methods available in the same database The database seeks to include FTIR El MS and accurate mass data on compounds of forensic interest Users can search the database from the Web without any other software and users are also encouraged to strengthen the database by contributing Quick Start Guide spectral data ee All databases are Web accessible with the ability to upload data sets for comparison or inclusion in the data library Download a tool to reformat Agilent Chemstation CSV files for use in the library Manage Mail _ Options For more information please contact RTI International s Center for Forensic Sciences or see our page of frequently asked questions You may also want to view the Quick Start Guide or the Introduction Presentation Email forensicdb rti org Spectra in ForensicDB should not be considered as published for the purpose of standard verification and should only be used as analytical tools RTI International and ForensicDB adhere to the SWGDRUG recommendation to run concurrent stan
13. d Note Formula example C10 Cl 1 10 F 0 N Exact Formula Weight example 120 3 or 20 50 Structure Search None v Perform search in all records Perform search in List A records only Spectrum Search FH Spectrum Similarity Search HH Spectrum Parameters HB User Data H v Spectrum Spectral method v Includes v EMS Spectrum Spectral method epe Spectrum Data reduction method CBS Spectrum Acquisition mode Spectrum Scan range 1D NMR Peaks EH Spectrum Sample introduction method Spectrum Mass calibration method H Spectrum Single compound or mixture Spectrum Orifice 1 voltage Spectrum Gas type Spectrum Gas flow rate Spectrum DART temperature Spectrum Mixture components Spectrum Notes Spectrum lonization mode Spectrum Mass measurement Spectrum Instrument type Spectrum Chromatography type Spectrum Tune type Spectrum Instrument make and model Spectrum Column Spectrum Injection port temperature Spectrum Transfer line temperature Spectrum Split ratio Spectrum Temperature ramp Spectrum Spectral resolution Spectrum Make and model of sampling access Spectrum Number of scans co added Spectrum Method and software used in data prc Spectrum Sample introduction phase Spectrum Fragmentation method y Figure 22 User Data search 18 ForensicDB A Web Accessible Spectral Database Saving Search Settings Specific searches can be saved for subsequent use by selecting the Save
14. dards of traceable reference materials to support identifications Part IV B Quality Assurance Section 2 3 Link http www swgdrug org Documents SWGDRUG 20Recommendations 206 htm amp PartlVB ReferenceMaterials Figure 1 ForensicDB Access page Upon entering the database the system will present a Login page that will ask you for a user name and password Figure 2 If this is your first time using ForensicDB you will need to create a free personal account To create an account e Select the Register option at the bottom of the Login page e Fill in the requested information and then click Register Once registered you will use your user name and password each time you log in to the system however note that on your first use of the system 1 e registration ForensicDB will take you directly to the default Database Home page and you can begin using the database immediatel y see Section 3 ForensicDB A Web Accessible Spectral Database Advanced Chemistry Development Please enter your credentials User Name fo Password fo Register Forgot your password Figure 2 ForensicDB Login page Users must login in to ForensicDB to access the system To login to the system e Enter your user name and password and click Log In e The system will then present two messages an automation message Figure 3 and a welcome message Figure 4 e Select OK for both messages The first message Figure 3 is a notification o
15. e default Database Home page are the Spectrum pane Spectrum Meta Data pane Molecular User Data pane Record Data pane and the Structure pane No further action 1s needed to view these panes as they are already displayed on the default Database Home page These panes are discussed further below c2 j Explore ff Database 4 Search Records OB E 4 ddd 4b 2 Vf Cm G9 BB of ES B searches v Ja 3128 3202 n 3202 DATA public_data SDB ID 3778 3128 3202 Stored Image dl 44 PP IP Spectrum Meta Data L 185 0000 Spectral method El MS Scan range 40 600 Mass calibration method PFTBA Single compound or mixture single compound Gas type He 3700000 385 0000 Notes 70 eV lonization mode positive 72 Mass measurement nominal Instrument type quadrupole Chromatography type GC Tune type auto tune Instrument make and model Agilent 5973 Relative Intensity 96 48 Method and software used in data processing averaged and Stored Image background subtracted 158 0000 r 40 1 Chromatographic method Column Rbx 5MS 30 m x 0 32 mm x 0 5 um Split ratio 15 1 Injection port temperature 300 C 32 114 0000 228 0000 300 0000 368 0000 386 000 Temperature ramp 240 C hold 1 min to 300 C at 30 C min hold 27 min 24 16 8 0 50 100 150 200 250 300 Record Data E Molecule User Data Submitted Name JWH 098 Formula C H _NO a SA 100 Structure e E 26 27 2 Notes LINK http Awww ca
16. ery Spectrum as a reference spectrum e Once the search is complete remember to deselect the mirrored reference as shown in Figure 10 Search Queries xa Search gl Clear Forms Main Search Form Spectrum Search Spectrum Similarity Search Figure 18 Spectrum Similarity search Select the Settings icon show in Figure 1 to change search settings This will allow you to show more or fewer search results based on the settings selected 15 ForensicDB A Web Accessible Spectral Database Under the Spectra Similarity tab select data type as MASS Figure 19 Selecting Include M ion is not recommended This option searches reference spectra e with the same most abundant peak in the last cluster as the query spectrum This does not search for a molecular ion e Changing the data type will allow for setting parameters for a FTIR spectrum similarity search e seo Mega os 000 R0 MASS y Structure Display Select Data Type Y Pl Include M lon Spectral Displa _ i Ad Y Use Minimal Similarity 50 Display Tolerance Structure Search All Similar 1 Spectra acc Da ppm Spectra Similarity Up to 10 F Quick Search Multiplet Search pet m Spectra Export wv OK X Cancel Figure 19 Search Similar Spectra settings Select the Search icon 2 to search the uploaded spectrum The Hit Qualtiy Index of the resulting spectra can be found in the Spec
17. est ForensicDB is organized into records and documents e Records are based off structure lot number and submitting facility Each record in the database contains information about the compound and submitting facility e Documents are spectra attached to each record and include instrumental parameters All documents within a record are from the same source lot same compound and same institution thus there may be several records for the same compound The following sections will provide instructions on accessing ForensicDB setting system parameters using the system navigating the system and comparing results 2 Accessing ForensicDB The ForensicDB Access page can be found at www forensicdb org Figure 1 To use ForensicDB you must use Internet Explorer 6 0 or greater In the near future ForensicDB will work with multiple web browsers It is recommended that you turn off the pop up blocker before accessing the website To enter the database select the Enter The Library link on the left sidebar of the ForensicDB Access page see orange box in Figure 1 ForensicDB A Web Accessible Spectral Database i wp nepre we NIJ ational p a Cheminformatics Database www forensicdb org INTERNATIONAI stice 286 30 T Ji O News RTI International has added several synthetic cannabinoids and cathinones to the database These items are spread throughout the database and can be searched by using the JWH
18. g Applet 17 ForensicDB A Web Accessible Spectral Database Conducting a Search of User Data Information related to alternate nomenclature and experimental parameters are searchable using the User Data field Figure 22 e Anything in the Record Data Spectrum Meta Data or Molecule User Data all of which are described in Section 3 is searchable in the User Data field e An update to ForensicDB search capabilities is in progress This new update adds the feature of a one click search option similar to a Google like search Searching by User Data information can be a standalone search For example users can search for all EI MS data of JWH compounds by setting the User Data field as follows e Spectrum Spectral method Includes EI MS e Select the sign to enter another search field such as And Submitted Name Includes JWH Searching by User Data information can be used in combination with a Spectrum Similarity search The User Data search can be used to narrow down the search to a particular instrumental technique For example users can upload an EI MS spectrum into the Spectrum Similarity search field and then set up the User Data field to search only within EI MS data as follows e Spectrum Spectral Method Includes EI MS ED P Explore Wi Database 4 Search Records amp e fif Search Queries A En A d Search wf Clear Forms Main Search Form H Multiple Database Search Current Database Search 9 Recor
19. mation e The returned results are displayed in order of RecordID not in order of Hit Quality Index as they are when searching through the ForensicDB interface The summary of returned results shows the records in order of decreasing Hit Quality Index to aid users in locating the top matches Users can perform subsequent searches from Agilent ChemStation They can navigate the database as described in Section 4 or review the results as described in Section 6 27 ForensicDB A Web Accessible Spectral Database 8 Submitting Spectra to ForensicDB Users can now upload their own spectra for inclusion in ForensicDB by going to the following Web Portal https www forensicdb org submit To submit spectra to ForensicDB e Choose whether you are submitting DART EIMS FTIR or OTHER spectral method Welcome to the spectrum submission form please begin by selecting the data type of the spectrum you are submitting If you cannot find submission forms appropriate for the data you wish to submit or have questions about data file support then please E mail forensicDBiprti org to request additional data accommodations EIMS Figure 36 Select data type to submit e Users must fill out a Record form providing information such as compound name submitting facility and submitter name Figure 37 Select whether you are submitting multiple files or a single file Selecting multiple files will keep all parameters the same so that
20. nly and will not impact use of the database ForensicDB A Web Accessible Spectral Database Message from webpage Cannot get client information because of the following reasons Automation server can t create object A welcome kmoore Figure 4 ForensicDB Welcome message Once you click OK for the two entry messages the default Database Home page will open automatically e The first time you enter ForensicDB the system will take you to the Explore tab within ForensicDB page shown below Figure 5 Double click on the DATA folder that is highlighted in Figure 5 This will then allow you to double click on the public_data SDB Once done it will open up the default Database Home page shown in Figure 9 which will allow you to set up your database settings see Section 3 Once completed the system will apply these setting to your user account so that this step does not have to be repeated each time ForensicDB is visited e For all return visits to ForensicDB after you have set up your settings the public database will automatically open to the default Database Home page see Section 4 Name Type public data SDB ACD SpecDB Enterprise Database Figure 5 ForensicDB Explore tab ForensicDB A Web Accessible Spectral Database 3 Setting System Properties This section describes setting two common system properties within ForensicDB The Spectrum properties are used to set the Spectral Display in order to view accur
21. o create a report of search results e Select the Create Report icon Figure 28 T i it i e P Explore j if Database Search Records x aja dq bb Ib b 4b E Ti Cm b io Figure 28 Create report 2 ForensicDB A Web Accessible Spectral Database Then choose to create the report in a HTML or PDF format Figure 29 El Choose the Report Format Webpage Dialog e Click the icon to get the report in HTML format Click the icon to get the repart in PDF formal Figure 29 Choose report format Finally select the items you want to show in the report Figure 30 Choose the Report Contents Webpage Dia PP nose the Report Contents Webpage Dig 7 E Clem All DATA Public_Data SDB Record ID 3811 E Submitted Name JWH 209 Synonyms 1 pentyl 2 methyl 3 4 methylphenylacetyl indole Submitter name Peter Stout Brian Thomas Jenny Wiley Submitter facility RTI Acquisition date 2011 2012 Standard source original JWH synthesis Standard original phase solid Class cannabimimetic Submitter email pstout rti org Barcode Record User Data Y Molecule Molecule User Data Formula C54 H5 NO FW 333 4666 InChk InChl 1 C23H27N0 c1 4 5 8 15 24 18 3 23 20 9 6 7 10 21 20 24 22 25 16 19 13 11 17 2 12 14 19 h SMILES Cc1ccc cc1 CC 2O c3c2ccccc2n CCCCC c3C InChl Key RDYZLFKKWNGIJS UHFFFAOYAE Figure 30 Select items to include in report 22 ForensicDB A Web A
22. od ti ED a 3 Figure 3 ForensicDB Login Automation MESSAg cccccccccnonocccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnonnnaninenoss 4 Figure 4 Forensic DB Welcome mesadas 4 Ligure 5 ForensicDB Explore 13D test OR anew aun eae nee eh eee eee 4 Figure 6 Settings for accurate mass on the Spectra Display Template sss 5 Figure 7 Analytical Data Type display on the Frame Properties page occcccccnnonoccccnnnnncncnnnananonnss 6 Fisure 5 Database 1COm desc EIDHODS ii 7 Figure 9 ForensicDB default Database Home page ccooooooooncnnncnnnononnnonnnnnnnnnononanannnnnnnnnnnnnnnninnnoss 8 Pi Sure 10 Spectrum View OPUS IA 9 Figure 11 Navigating between spectra within a record o0ooooonnnnnncccnnnnncnnnnnnnnnnnonononnnnnnnnccnnnnnnnnnonoss 10 Pieure 2 Spectrum Meta Dala pan 10 Ersute SS TUI DAMA eii 11 11 Figure 14 Figure 15 Figure 16 Figure 17 Figure 18 Figure 19 Figure 20 Figure 21 Figure 22 Figure 23 Figure 24 Figure 25 Figure 26 Figure 27 Figure 28 Figure 29 Figure 30 Figure 31 Figure 32 Figure 33 Figure 34 Figure 35 Figure 36 Figure 37 Figure 38 Figure 39 ForensicDB A Web Accessible Spectral Database R cord Data Pane sal TEM 12 Molecule User Dala Pa o epua EE A O ART 12 eaten Record TD dad dd eddie 13 Mati SC Ate hi FO eie ia 13 Spectrum Similarity SC sica e e aia 15 Searchosimilar Spectra Seno a a nda ede eee 16 DIEUCTUEE SS e eec abate top ad a EE
23. ration file that stores user search settings After copying the macros executable and configuration files into the correct directories close and re launch Agilent ChemStation Data Analysis software Creating a JCAMP file from Agilent ChemStation While displaying a spectrum hold the lt control gt key down and double right click with the mouse Figure 31 A JCAMP file of the displayed spectrum is created and automatically saved in the c msdchem ForensicDB directory MSD ChemStation 3 xj ForensicDB C msdchem ForensicDB 02201204 0 Average of 29 719 to 29 885 min jdx file has been created i Cancel P e Search similar spectra in ForensicDB Figure 31 Notification of created JCAMP file Select Cancel in Figure 31 if you do not have Internet access at the instrument computer You can then take the created JCAMP spectrum from the c msdchem ForensicDB folder and search it on an Internet capable computer as described in Section 5 Conducting a Spectrum Similarity Search e The created JCAMP file name will include the file name of the D data file from which it was created with the averaged retention times added to the end In the case shown in Figure 31 the original data file was 02201204 D and the exported spectrum was an average over 29 719 to 29 885 minutes e The JCAMP file does not contain any information that may have been embedded in the data file when acquiring data on the instrument It only contains the title
24. rch For example say you search a FTIR spectrum of an unknown sample and it returns 30 results You can then narrow down those search results by uploading an EI MS spectrum of that same unknown sample and selecting the Perform Search in List A records only option This search will be restricted to the previously returned records with matching FTIR spectra therefore all results will have both matching FTIR and EI MS spectra There are several important tasks to remember when performing subsequent searches within the database e Within the Database tab make sure to select the All icon to reset list A to all records in the database before performing another search This is done to ensure that you are searching within all records in the database and not the returned results from a previous search Clear Forms e Make sure to select the Clear Forms icon within the Search Records tab before performing another search This will clear all information within the Search Records tab to their default settings and clear any uploads from a previous search 14 ForensicDB A Web Accessible Spectral Database Conducting a Spectrum Similarity Search Use the Spectrum Similarity search field to upload a spectrum Figure 18 e Acceptable file formats include JCAMP jdx dx ACD Labs spectrum esp netCDF cdf nc JEOL jsp jdf Nicolet OMNIC spa spg Perkin Elmer IR Data Manager sp Thermo Galactic spc Check the box to Set the Qu
25. rent Structure searches for other records with the same exact structure Search Substructure searches for records with the same substructure as the one currently displayed and Search Structure Similar to Current searches for records in ForensicDB based on structural similarity For example 1f you are looking at a record for JWH 018 selecting Search Current Structure will return all records for JWH 018 in ForensicDB Selecting Search Structure Similar to Current will return all records with structures similar to JWH 018 likely many related JWH compounds 9 E El 100 HH Tile View ES Table View g Open in Window Copy Divide Vertically EH Divide Horizontally X Remove Frame Properties E Save Layout E Load Layout y Manage Layouts amp Search Current Structure 32 Search Substructure Search Structure Similar To Current Figure 13 Structure pane 11 ForensicDB A Web Accessible Spectral Database Record Data Pane The Record Data pane provides information on the submitted compound submitting institution and source material Figure 14 Record Data submitted Mame JWH 098 Notes FLINK httpiwww caymanchem com app template Productvm catalagq 10680 synonyms 1 pentyl 2 methyl 3 4 methoxy 1 naphthoy indole submitter name Paul Kennedy Submitter facility Cayman Chemical Acquisition date 2011 2012 standard source Cayman Chemical lot 0427192 Standard original phase solid Cl
26. rs must back up their original mouse mac macro especially if they created their own custom mouse actions The below directions will overwrite your current mouse mac macro located in the c msdchem msmacros directory RTI International is not responsible for any loss or damage These macros are supported on Agilent ChemStation versions G1701EA version E 00 E 02 and G1701DA version D 02 D 03 There are two installation options 1 Install macros executable file and configuration file automatically using the provided installation package a This will copy the macros and application to the hard drive b The installation assumes that Agilent ChemStation is installed on the c drive 2 Manually download and install the two macros and two applications that allow creation of a JCAMP file and facilitates ForensicDB spectrum similarity search from Agilent ChemStation a Copy the mouse mac macro into the c msdchem msmacros directory 23 ForensicDB A Web Accessible Spectral Database 1 This is a system macro that was modified to create a custom mouse action il Users must create a backup copy of their original mouse mac macro especially 1f they created their own custom mouse macro functions b Copy nes_jcamp mac WLquery exe and WLWSSettings ini into the c msdchem msexe directory 1 nes_jcamp mac and WLquery exe create the JCAMP file and pass it to ForensicDB for spectrum similarity searching 1 WLWSSettings 1s a configu
27. ssible Spectral Database 9 Contact Information We are available to answer questions or provide support Monday through Friday 8 15 AM to 5 00 PM EST excluding holidays You may contact us by phone fax email or letter Phone 1 866 252 8415 Fax 919 541 7042 Email forensicdb Orti org Letter 3040 E Cornwallis Rd P O Box 12194 Research Triangle Park NC 27709 30
28. trum Meta Data pane Figure 12 Section 4 16 ForensicDB A Web Accessible Spectral Database Conducting a Structure Search Users can search structure by exact similarity or substructure by selecting the desired search criteria in the Structure Search dropdown box Figure 20 You will not be able to view or upload a structure as shown in Figure 20 until a Structure Search option is chosen from the dropdown box The Hit Qualtiy Index of the resulting structures can be found in the Molecule User Data pane Figure 15 Section 4 CD P Explore Database Search Records Search Queries E A Main Search Form H To enter a new structure or edit the entered one uble click the box below Multiple Database Search Current Database Search 9 O Record Note e 2 Formula example C10 Cl 1 10 F 0 N Exact gt LN N Formula Weight example 120 2 nr 2N Any Structure Search Similarity Y 9 Perform search in all records A Perform search in ListA records only Figure 20 Structure Search There are two ways to display a structure to search in the database e Upload an existing structure only MOL file format accepted using the upload icon e Draw the structure using the Drawing icon The Drawing icon displays a Drawing Applet Figure 21 a Draw Structure Webpage Dialog LIB e WM slaja a 9 le BRIT Ie e 2 2 INNDS Figure 21 Drawin
29. ttings Select Search to initiate the ForensicDB spectral similarity search If you have not logged into ForensicDB you will be prompted to log in Once logged in you will see a Webpage dialog box showing the number of records found Figure 34 and a summary of the returned results in a Notepad document Figure 35 B Info Webpage Dialog X 2 9 records were found ff OK Figure 34 Number of records found 26 ForensicDB A Web Accessible Spectral Database fh Untitled Notepad ini xl File Edit Format View Help similarity Search results for the spectrum C msdchemsForensicDB02201204 D Average of 29 726 to 29 853 min jdx 1 ID 3825 Spectrum No 6 HQI 0 00 compound JWH 073 2 naphthyl N 1 methylpropyl isomer ID 3330 Spectrum No l HQI l Compound JwH 073 1 ID 3089 Specjtrum No HQI 33 Compound JwH 073 1 ID 3911 spectrum No HOI 61 compound Ultra Cloud 10 3889 Spectrum No TO HQI 61 26 Compound Happy Shaman Humboldt Gold 4c 3308 Spectrum No HQI 33 Compound JwH 015 3097 Spectrum No HQI 83 Compound JwH 015 3888 spectrum No HQI 7 65 Compound Happy Shaman Herbs Pink Tiger 3892 spectrum No FG HQI 42 Compound JwH 018 N 1 methylbutyl 1somer Figure 35 Summary of returned results The purpose of the summary of returned results is to show the Record ID number the Spectrum number the Hit Quality Index and the Compound name This provides users with a quick view of all infor
30. x so that the box remains blank see orange box in Figure 7 e Then click OK Frame properties Webpage Dialog Name Spectrum Show Name Frame Type Spectrum Show Toolbar 47 Analytical data type el Frame order 1 E By Spectrum User Data E Keep zoom Shaw Next Prev set of s pectrum buttons 1DMME HQI ff OK X Cancel Figure 7 Analytical Data Type display on the Frame Properties page ForensicDB A Web Accessible Spectral Database 4 Navigating the Database Navigation Tools ForensicDB provides numerous icons that you can use to navigate the database Figure 8 shows the major database icons used in ForensicDB as well as a description of each icon s function Main Tool Bar Functions Main Tab Description Y Show all database records 9 Explore Log on default screen Next record or document fff Database Navigate database Last record or document 4 Search Records Search database Locate a specific record ID Help manual Database must be open to perform task Figure 8 Database icon descriptions ForensicDB A Web Accessible Spectral Database Using the Default Database Home Page A screen shot of the default Database Home page is shown in Figure 9 The default Database Home page presents a number of panes to help users to easily view spectral data structure instrumental parameters and information about the compound such as its source material The panes shown on th
31. ymanchem com app template Product vm catalog 10680 FW 385 4981 NNI FO a ae kre THE InChl InChl 1 C26H27NO2 c1 4 5 10 17 27 18 2 25 22 13 8 9 14 23 22 27 26 28 21 15 Submitter name Paul Kennedy 16 24 29 3 20 12 7 6 11 19 20 21 h6 9 11 16H 4 5 10 17H2 1 3H3 Submitter facility Cayman Chemical SMILES COc2ccc ctccccc12 C O c4c3ccccc3n CCCCC c4C Acquisition date 2011 2012 InChl Key CNTCHEBQQFICNR UHFFFAOYAS Standard source Cayman Chemical lot 0427192 Molar Refractivity 117 8140 5 cam Standard original phase solid 3 Class Cannabimimetic Molar Volume 348 8 7 0 cm Submitter email custserv caymanchem com Parachor 875 4 8 0 cm Index of Refraction 1 590 0 05 Surface Tension 39 6 7 0 dyne cm Density 1 10 0 1 g cm Dielectric Constant cannot calculate Polarizability 46 70 0 5 10 2 cm Monoisotopic Mass 385 204179 Da x Figure 9 ForensicDB default Database Home page ForensicDB A Web Accessible Spectral Database Spectrum pane The Spectrum pane shown in Figure 10 shows the spectral data Data that can be viewed within the Spectrum pane include nominal mass accurate mass FTIR and chromatographic data dll a dd Pb ID Spectrum MASS Sealy 185 00004 T p E D E m m 3 r3 BU 3 x Zoom Qut Tile View Table View Open in Window Divide Vertically Divide Horizontally Remove Frame Properties Save Layout Load Layout Manage Layouts gt m EXOK M H
32. you do not have to re input the parameters each time Submitter name Acquisition date Standard orginal phase Data type Multiple or single files Figure 37 Enter record information 28 ForensicDB A Web Accessible Spectral Database e Select Next once the record information is completed The next screen Figure 38 is used to enter specific instrumental parameters Uploaded files must be averaged and background subtracted Instrument type Quadrupole single or multiple y Chromatographic method include split ratio temperature ramp column and dimensions injection port temperature gas type and retention time Method and software used in data processing example averaged and background subtracted MassCenter v 1 3 6e Notes please detail any responses where you chose other and add additional comments parameters as needed Figure 38 Enter instrumental parameters Once your data are submitted you will receive a notification of your submission that asks whether you want the instrumental parameters to stay the same for each subsequent submission Figure 39 Thank you Your file and data have been submitted Do you want to upload more records using the field values you have input for this record Figure 39 Notification of submitted data If you would like to submit data for a specific spectral method that 1s not represented in the Web portal please contact us 29 ForensicDB A Web Acce
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