MolFind User Manual - University of Connecticut
Contents
1. C13H11 0 7736 4 0 375 s 6 300 34 2 29 53134893 337 019 C13H11 0 6957 5 0 125 12 2 326 8 1 86 20923018 337 019 C13H11 0 6494 6 0 125 12 2 327 Fa woke 52480092 337 019 C13H11 0 6287 7 0 0 141 0 341 7 1 38 9927768 337 019 C13H11 0 6145 8 0 3125 6 5 289 45 2 74 16639946 337 019 C13H11 0 6142 9 0 3125 6 5 290 44 2 76 21254965 337 019 C1l3H11 0 6005 10 0 0 141 0 313 21 1 52 43546233 337 022 C10H15 0 5823 11 0 0625 35 1 297 37 1 29 44461906 337 019 C13H11 0 5822 12 0 0 141 0 310 24 1 58 9306181 337 019 C13H11 0 5748 13 0 0 141 0 327 7 1 94 43828481 337 019 C13H11 0 574 14 0 0 141 0 338 5 0 98 70222830 337 019 C13H11 0 5651 15 0 0 141 a a gt 13 Select the experimental spectrum located under TestCalculations folder 14 Click on Run MetFrag button to rank candidates 10 MolFind Ouput Files 7 MolFind Ouput Files Kee ee e pereen mnan Pn TXT BioSM_Files fragments1 fragments2 inputTo3DOptimiz molconnin sdf molconnOut txt er sdf csv csv TXT tenoxicam_filtered tenoxicam_MetFrag tenoxicam_MetFrag tenoxicam_MetFrag tenoxicam_MetFrag tenoxicam_out txt sdf Run_l csv Run_l json Run_2 csv Run_2 json GZ tenoxicam sdf gz BioSM Files Input Output files for BioSM program predicts whether a compound is biological or not fragments1 fragments2 MetFrag predicted fragments for two MetFrag runs inputTo3DO2. kcal mol higher than the lowest energy conformer When you click on the Convert button a new directory named 13 Running Mobcal Calculations mobcalData will be created in the directory of the SD file Mobcal input files will be stored in the mobcalData directory Steps 2 4 Generate Gaussian input files from 2D SD file s SDF To Gaussian Input No of Processors 4 Gaussian Commands n B3LYP 6 31G Opt maxcycles 200 nosymm pop chelpg Convert Step 6 Gaussian output to Mobcal input Mobcal Parameters Charge Method Uniform Charge ia Select Mobcal charge method Gaussian Output To Mobcal Input Gaussian Output Files Directory Open Convert Select a directory to store Gaussian input files Click on the Convert button to generate Gaussian input files Step 7 Run Mobcal Run Mobcal Mobcal Executable Users lochana EclipseProjects mobcal bin mobcal_N2 Open Molcal Input Files Directory Open Run Compile Following the compilation instructions in the ReadMe txt file the Mobcal source code located in the Mobcal directory Select the Mobcal executable and Mobcal input files directory Click on the Run button to run Mobcal in parallel Mobcal output files will be found in the mobcalData directory Please Note Both ionic form generation and MM charge generation algorithms require separate ChemAxon licenses Make sure to have valid ChemAxon licenses for p
3. Password Current Lhasa members can request a username and password to access IIMDB Please contact Mr Scott McDonald at Lhasa Ltd for a user account Scott McDonald lhasalimited org RI ECOM50 and Drift Time Windows Model Windows for filtering candidate compounds 12 Running Mobcal Calculations 9 Running Mobcal Calculations MolFind s Tools panel provides several utilities to prepare Mobcal Gaussian input files and run Mobcal calculations in parallel Mobcal input files can be prepared from 2D SD files or Gaussian G03 or G09 output files Please refer to the numbered steps in the following figure 2D SD File 2D SD File e 2 gt 3D SD File Gaus sian Gaussian Mobcal Mobcal Input Output Input Output Step 1 Convert the SD file to M H M H or M Na form Select SD File Open Convert SDF Structures to Step 2 3 Generate Mobcal input file s using molecular mechanics optimized structure s Mobcal Parameters Charge Method Uniform Charge ix Select Mobcal charge method SDF To Mobcal Input No of Conformers 1 hea Energy Cutoff kcal mol 2 l Convert Select the number of conformers and energy cutoff If number of conformers this is the maximum possible number of conformers is set to more than 1 multiple conformers will be used An energy cutoff of 0 will use however many structures that conformer generation comes up with An energy cutoff of N will remove any conformer that is N
4. Search a Results E Search By Exact Mass 337 0191 TL a cl N ia Mass Accuracy 10 PPM v s yn Search PubChem Search IIMDB Search Name Formula 4 2 2 chloropyrimidin 4 yl cyano C16H8CIN5S V Human Compounds Stereoisomers 74345410 337 018 Plant Compounds 74224458 N 5 ethyl 1 3 4 thiadiazol 2 yl 4 C11H10F3N302S2 337 016 74059370 iridium 1 phenyl 1 2 4 triazole C8H6IrN3 337 019 W Drugs 74031325 5 6 bis 4 chlorophenyl 1 2 4 triazin C15H13CI2N3S 337 020 7 Lipids 73990583 benzene palladium C18H15Pd 3 337 020 73987651 7 3 bromo 4 methylphenyl 1 2 3 7 C12H12BrN502 47 017 73979911 4 amino 2 3 chloro 2 fluorophenyl C13H9CIFNSOS 337 020 73840635 5 4 bromophenyl hydrazinylidene 6 C12H12BrNSO2 gic rh br ae Local SDF MolGen 5 0 PMG Open 73827710 1 2 3 dioxo 6 trifluoromethyl quino C11H9F3N205P 337 020 73729678 chloroplatinum 1 cycloocta 1 5 diene C8H11CIPt 337 019 Search SDF Search 73777698 5 6 0xo 3H pyridazin 3 yl N thio C13H11N304S2 337 019 73777342 N furan 2 ylmethyl 5 6 oxo 3H p C13H11N304S2 397 Us 73711905 ethyl 2 pyrazol 1 id 3 ylacetate tung C7HIN2ZO02W 337 017 V Remove Disconnected Structures 73700946 methyl 2 4 dimethyl 3H pyrazol 3 id C7HIN2ZO2W E eo F 73700945 methyl 1 4 dimethyl 3H pyrazol 3 id C7H9N202W 337 017 V Remove Heav
5. editing MolFind bat or MolFind sh file See FAQ for more details Processor There is no processor requirement However faster multicore processors will certainly help MolFind can take advantage of modern multicore architectures Installation Instructions 3 Installation Instructions No installation required Simply extract the downloaded zip file into a folder If you are on Windows Windows XP Windows Vista or Windows 7 8 8 1 double click on the MolFind bat file to start MolFind If you are on Mac OSX Linux or Solaris double click on the MolFind sh file to start MolFind Double clicking MolFind jar should also work User Interface 4 User Interface MolFind comes with a tabbed graphical user interface TGUI eoo MolFind 1 9 LC MS Based Identification of Chemical Structures in Biofluids Job Setup Compound Search and Filter Compound Identification Tools Analysis Compound Search a Results Search By Exact Mass 337 0191 i N N AA 4 cl N i Mass Accuracy 10 Pem jw s N Search PubChem Search IIMDB Search lt W Human Compounds Stereoisomers Name Formula 74345410 4 2 2 chloropyrimidin 4 yl cyano C16H8CIN5S SSF Ue Bess V Plant Compounds 74224458 N 5 ethyl 1 3 4 thiadiazol 2 yl 4 C11H10F3N30252 337 016 T 74059370 iridium 1 phenyl 1 2 4 triazole C8H6IrN3 337 019 Drugs 74031325 5 6 bis 4 chlorophenyl 1 2 4 triazin C15H13CI2N3S 337 020 G Lipids 73990583 benz
6. 134 COMPOUND_IDENTIFICATION_RUN_3 215 9784 140 552 274 0677 135 659 302 0068 102 238 338 0271 1545 029 lt Candidate ID IIMDB00005175 164 0821 215 9784 o 274 0677 ID MOLFIND_SCORE MOLFIND_RANK NO_OF_PEAKS_MATCHED IIMDB00003478 0 623 2 1 IIMDBO0005055 0 576 3 IIMDB00005175 0 825 l IIMDB00091613 0 521 4 Analysis panel allows you to analyze results from a previously ran MolFind job Simply load the MolFind output _out txt file using Open button If your MolFind job has multiple MetFrag runs they will show up as a list as shown in figure above The data for currently selected MetFrag run will be shown on the tables 16 FAQ 11 FAQ 1 How do I change the amount of memory allocated to java virtual machine Open the startup script MolFind bat or MolFind sh with a text editor Change the highlighted number to desired amount Xmx1g 1g 1 GB g stands for giga bytes Recommended free text editors Windows Notepad http notepad plus plus org Komodo Edit OSX TextEdit TextWrangler Komodo Edit Linux gedit 2 What happens when I double click on the startup script not the jar file to start the program Memory allocation information is passed on to java virtual machine via startup scripts 3 What happens if I don t select a working directory for my calculations By default output file
7. Ka and charge modules installed Citing MolFind and Mobcal 14 Running Mobcal Calculations Please cite Mobcal N2 Optimized Mobcal and MolFind by adding a statement similar to this All structure manipulations generation of ionized forms and molecular mechanics based conformers and input file preparations for gaussian09 and Mobcal were done using MolFind s 12 4 tools panel A modified version of Mobca optimized for room temperature N2 based trajectory method TM was used for calculating average collision cross sectional areas 1 Menikarachchi L C Cawley S Hill D W Hall L M Hall L Lai S Wilder J Grant D F Anal Chem 2012 84 9388 93394 2 Campuzano I Bush M F Robinson C V Beaumont C Richardson K Kim H Kim H I Anal Chem 2012 84 1026 1033 3 Mesleh M F Hunter J M Shvartsburg A A Schatz G C Jarrold M F J Phys Chem 1996 100 16082 16086 4 Shvartsburg A Chem Phys Lett 1996 261 86 91 Analysis Panel 10 Analysis Panel e090 MolFind 1 8 LC MS Based Identification of Chemical Structures in Biofluids Job Setup Compound Search and Filter Compound Identification Tools Settings Analysis About MolFind Output Analyzer Select MolFind Output Users lochana Desktop Job1 Job1_out txt COMPOUND_IDENTIFICATION_RUN_1 164 0821 3061 426 _COMPOUND_IDENTIFICATION_RUN_2 169 9755 367 048 199 9832 1383
8. MolFind User Manual MolFind 1 9 06 18 2014 M F Lochana C Menikarachchi Ph D Department of Pharmaceutical Sciences School of Pharmacy University of Connecticut Introduction 1 Introduction MolFind is a java based software package for identifying unknown chemical structures in complex mixtures using HPLC MS data Identifying an unknown involves matching orthogonal experimental features measured for the unknown RI ECOMS5S0O drift time and CID spectra with computationally predicted values for candidate compounds contained in chemical or biochemical databases The program features an easy to use graphical user interface and a highly multi threaded pipeline for identifying unknowns System Requirements 2 System Requirements Operating System MolFind should work on any operating system Windows XP Windows Vista Windows 7 8 8 1 Mac OSX Any version of Linux or Solaris provided java 1 6 or higher is installed Java standard edition SE run time jre 1 6 jre 1 7 can be freely downloaded from http www oracle com technetwork java javase downloads index html Memory We recommend 1 2 GB of RAM for java virtual machine however more RAM may be required depending on the type of calculation Bundled program execution scripts MolFind bat for windows and MolFind sh for linux osx solaris will allocate 2 GB of RAM for the java virtual machine The amount of RAM allocated for java virtual machine can be changed by
9. dates using MetFrag algorithm Various tools to generate Gaussian Mobcal input Tools files etc Various settings such as QSPR model windows Settings passwords etc Analyze visualize MolFind output file _out xt Licensing terms and references By default MolFind loads first 100 candidates into the table on the Compound Search panel If User Interface your filters resulted in more than 100 structures the rest will not show up in the first page Please use the page down up buttons buttons located under the magnifying glass icons in the figure above to load next previous 100 candidates The table on the Compound Identification panel behaves similarly Both tables one on the search panel and the one on the identification panel do not allow sorting The table on the Analysis panel allows sorting Contents of the MolFind Folder 5 Contents of the MolFind Folder T _ D X wr r panoan ansasen BAT JAR perene config Licenses MolFind_User MolFind bat MolFind jar lib Manual pdf MolFind sh TestCalculation Mobcal config configuration files Licenses licenses for third party libraries MolFind_UserManual pdf this document MolFind bat program startup script for windows MolFind jar MolFind platform independent executable lib third party libraries MolFind sh program startup script for osx linux or solaris TestCalculation data for test calculations Mobcal Mobcal source files and compilation ins
10. ene palladium C18H15Pd 3 337 020 p 73987651 7 3 bromo 4 methylphenyl 1 2 3 7 C12H12BrN502 E aa iF 73979911 4 amino 2 3 chloro 2 fluorophenyl C13H9CIFN50S 337 020 73840635 5 4 bromophenyl hydrazinylidene 6 C12H12BrN502 SAFNI Local SDF MolGen 5 0 PMG W Open 73827710 1 2 3 dioxo 6 trifluoromethyl quino C11H9F3N205P 337 020 73729678 chloroplatinum 1 cycloocta 1 5 diene C8H11CIPt Jap Search SDF Search 73777698 5 6 0ox0 3H pyridazin 3 yl N thio C13H11N30452 337 019 73777342 N furan 2 ylmethyl 5 6 oxo 3H p C13H11N304S2 337 019 73711905 ethyl 2 pyrazol 1 id 3 ylacetate tung C7HIN2ZO02W 337 017 V Remove Disconnected Structures 73700946 methyl 2 4 dimethyl 3H pyrazol 3 id C7HIN2ZO2W 337 017 73700945 methyl 1 4 dimethyl 3H pyrazol 3 id C7HIN2ZO2W 337 017 V Remove Heavy Isotopes 73708705 3 3 4 chlorophenyl sulfamoyl pheny C1SH12CINO4S Cie He Were i 73549344 N S 3 nitrophenyl methylidene 4 C13H11N30452 337 019 V Remove Stereoisomers 73497938 4 amino 4 oxo 2 4 oxo 5 pyridin C13H11N30452 337 019 Keen Comoommds With 14684564 1 3 dimethyl 8 pyridin 1 ium 1l yl 7 C12H12BrN502 337 017 p p 73497937 4 amino 4 oxo 2 4 oxo 5 pyridin C13H11N30452 337 019 MH Ac MNMOMeP Ms OF Cael 73471927 cyclopenta 1 3 diene phenoxychloran C17H15CIO2V 337 0290 7 a y Compounds Must Contain Exact Mass Query Resulted in 1433 Hits Rank identify candi
11. ompounds have been downloaded The selected filters will be applied as soon as you hit the Apply Selected Filters button Running Calculations 10 Apply filters Elements Disconnected Structures RI ECOMS50 Drift Time once the download is complete 11 Click on Proceed to Identification button once the filtering process is over 12 Switch to Compound Identification panel MolFind 1 7 LC MS Based Identification of Chemical Structures in Biofluids 800 Job Setup Compound Search and Filter Compound Identification Tools Settings Analysis About CID Spectrum 10 000 7 500 o 5 000 Lan 2 500 a 100 150 200 250 300 350 m z Experimental Spectrum Mode M H M H M Charge O Positive Negative Mzabs 0 Mzppm 10 beg Fragmentation Tree Depth 2 S Neutral Loss Rules in Every Layer _ Run MetFrag Compound Identification Completed Results cs s oa N N n Oo Oo X ZA N N a a o o Na NS o NS o NA 95 0611 121 04 164 0821 o oO W N N S Pau N N ao a A o NA o NA 164 0821 164 0821 Las sres ID MIMW FORMULA MOLFIND MOLFIND CID SCORE CID RANK PEAKS M RI ARI ECOM50 a SAZLALOZ S337019 GISHLI a 54677971 337 019 C13H11 0 8083 2 0 375 s 6 301 33 2 09 54694107 337 019 C13H11 0 7768 3 0 375 4 6 300 34 2 27 54694108 337 019
12. ptimizer sdf 2D structure input file for geometry optimizations molconnIn sdf Input file for Molconn molconnOut txt Calculated RI and ECOMso values tenoxicam_filtered sdf filtered candidates for tenoxicam bin tenoxicam_MetFragRun_1 csv tenoxicam_MetFragRun_ 2 csv Results for two MetFrag runs in csv format does not include MetFrag fragments tenoxicam_MetFragRun_1 json tenoxicam_MetFragRun_2 json Results for two MetFrag runs in json format Include MetFrag fragments tenoxicam_out txt Output file for the MolFind job can be visualized with Analysis Panel tenoxicam sdf gz candidates downloaded from PubChem 11 Settings Panel 8 Settings Panel i e090 MolFind 1 7 LC MS Based Identification of Chemical Structures in Biofluids Job Setup Compound Search and Filter Compound Identification Tools Settings Analysis About Drift Time Model Users lochana Work_Pharmacy GrantLab_Software MolFind config dModel pmml Select IIMDB Username grantLabUser IIMDB Password _Set Credentials RI Window 114 2 ECOM50 Window 2 1 b n Drift Time Window 0 35 Set Windows No of Processors 4 Maximum Memory Available to JAVA Virtual Machine 1820 MB Current Windows RI 114 ECOMSO 2 10 Drift Time 0 35 Drift Time Model PMML Predictive Modeling Markup Language file containing drift time model this file is usually located under config folder IIMDB Username and
13. s will be saved in tempMolFind folder located under user s home directory However using tempMolFind is not recommended except for testing files in tempMolFind folder are deleted at the startup 4 I don t see the CID number of my target in the identification panel Sometimes MolFind can list a different stereoisomer than your target Look Under PubChem StereIsomers column as well 5 Nothing happens when I double click MolFind bat This happens when operating system cannot locate the java run time jre Add C Program Files x86 Java jre7 bin Or 17 FAQ C Program Files Java jre7 bin to windows path jre might be found at a different location Look for jre6 bin or jre7 bin directories on your system 6 How do I know java runtime is correctly installed and java path is correctly set Type java version at the command prompt dos prompt in windows or terminal in osx linux This command should return the version number of java runtime 7 I have a question How do I contact the authors You can use either the contact form on the web site or MolFind google page for submitting questions 18
14. tructions MolFind log This file is created at the startup MolFind log contains logging information for the current MolFind session Check the log file for any errors If logging is disabled the MolFind log file will not be created 4 L leva Control Panel Oo General Update Java Seartty AGranced Deducorg Enade traong LAE AAAA Enade D99 Show agpiet bfecyce excepniors Follow the instructions on http www java com en download help javaconsole xml to locate java control panel Click on the Advanced tab and check the Enable logging option Running Calculations 6 Running Calculations 1 Go to Job Setup tab 2 Type in a name for the job All data for the job will be saved in a sub directory 3 Select a working directory for MolFind calculations All jobs will be stored inside the working directory MolFind 1 7 LC MS Based Identification of Chemical Structures in Biofluids eoo Job Setup Compound Search and Filter Compound Identification Tools Settings Analysis About Job Name tenoxicam Select Working Directory Users lochana Desktop Your calculation results are stored in Users lochana Desktop tenoxicam 4 Click Save Current Job label will change to your job folder 5 Go to Compound Search and Filter tab Running Calculations e090 MolFind 1 9 LC MS Based Identification of Chemical Structures in Biofluids Compound Search and Filter Compound
15. y Isotopes 73708705 3 3 4 chlorophenyl sulfamoyl pheny C1SH12CINO4S 337 017 73549344 N 5 3 nitrophenyl methylidene 4 C13H11N304S2 337 019 Yj Remove Stereoisomers 73497938 4 amino 4 oxo 2 4 oxo 5 pyridin C13H11N304S2 337 019 Keep Compounds With 14684564 1 3 dimethyl 8 pyridin 1 ium 1 yl 7 C12H12BrNS0O2 337 017 73497937 4 amino 4 oxo 2 4 oxo 5 pyridin C13H11N30452 337 015 MHM cMnMowme Ms Of Cate 73471927 cyclopenta 1 3 diene phenoxychloran C17H1SCIO2V 337 020 lt Compounds Must Contain Y Exact Mass Query Resulted in 1433 Hits 6 Type in the neutral exact mass or accept the default value for test calculation provided Note that MolFind currently allows users to search for a single unknown Future versions will allow batch processing of multiple unknowns 7 Select the mass accuracy in ppm or ppb MolFind is designed for high mass accuracy data 1 20 ppm and thus there is a limit to the number of candidate compounds that can be downloaded for any given mass 8 Click on the appropriate search button to download compounds from PubChem IIMDB or a local SD file Exact Mass Query Resulted in 953 Hits 9 The Status bar at the bottom of the screen will show the progress of the calculation and whether any errors occurred during the calculation Real time status updates will be delivered through the status bar Please note that no filters are used until after the c
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