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SmileMS user manual

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1. profile for demo F Tolerance in high mass accuracy scoring Da 0 04 Update mu default profiles are used in certain integration processes Typically they are used to ensure the use of a unique profile throughout technicians of a laboratory License configuration The license configuration is the part of the administration workspace that is used to to obtain information about the currently used license or to renew it The About tab shows The current version number of SmileMS Alinkto the license agreement General information and copyright about GeneBio About license information Version number 1 1 12 License agreement Copyright notice for SrmileMs SmileMS is developed by Geneva Bioinformatics GeneBia 5 6 All intellectual property rights on SmileMS belong to GeneBia Copyright amp 2010 GeneBio All rights reserved GeneBia 25 Avenue de Champel CH 1706 Geneva Switzerland Ge NEBIO The License information tab shows SmileMS user manual 46 v1 2 May2011 The Host id of the computer on which SmileMS is installed this number is required for all interaction with GeneBio and the customer support An option to renew a license Asummary of the license scope About License information Host id 16770424 Renew license Upload file Status for xrank submission Wendor unknown mdata 18 08 2010 hostid 16770424 counted uncounted Wersian 1 days 30 licence type permanen
2. database http pubchem ncbi nim nih gov with the name of the Compound and opens a new window with the results of the query This functionality is searching via internet and is only available if you have access to Internet name admin admin SENEBIO A Exit 6 Sm ile MS Analysis Library Administration N Hel A Library list demo for install 2 Refresh Chemical compound Acetaminophen Benzoylecgonine Cocaine spectra at 3 8 Cocaine m z MS level 304 15 2 0 6 D3 Chlorpromazine D3 Clomipramine D4 Haloperidol Desipramine Diazepam Flecainide Hydrocortisone MDMA Metamphetamine Methadone Metoprolol Olanzapine Paracetamol Cocaine Cocaine Cocaine Cocaine Cocaine Cocaine 304 15 304 1 304 1 304 1 304 1 N O O N N N 304 15 Chemical compound Spectrum name Molecular ion m z Precursor m z Retention time min MS level Polarity CAS Synonyms Fo Export reset zoom vrescale Reference spectrum 60 80 100 120 140 160 180 m z Da Reference spectrum 120711 Cocaine Cocaine 304 1544 304 1544 0 82 2 50 36 2 edit delete Paroxetine Risperidone Show compound in PubChem Sotalol Venlafaxine 0 N F N E A WN BD UO fF FF FP oF YN OD W P Zolpidem Modify a library entry You may need to change a spectrum annotation in a library such as adjusting the Retention ti
3. db0i Description small test Do you want to import yes spectra from a library file e moa aca gt create x cancel smoiall dbO1 created 0 spectra A pop up appears that says the library is created You can add experimental spectra to this library from the edition fields in the results pages See the Spectrum viewer section for more details If you want to import spectra to the newly defined library select yes SmileMS user manual 36 v1 2 May2011 New library Name small dbO1 Description small test db Do you want to import e ves spectra from a library file L J ne Ls imi Upload library file size bytes 115 296 complete You are asked to upload a library file Browse your computer for the library to be imported and click Upload library file Once uploaded click on create to create the library in SmileMS New library Hame Description Do you want to import spectra from a library file processing library A progress bar appears and the interface is blocked for other actions during the library preparation step This might take a few minutes or up to over an hour depending on the number of spectra in the library to upload At the end of the process a completion pop up window appears containing the name of the library and the number of stored spectra SmileMS user manual 37 v1 2 May2011 small dbQi created 44 spectra The library is then visible in the Library li
4. of the best matching spectrum for this compound Delta RT Retention time difference between the value in the best matching spectrum and the corresponding value annotated for the reference spectrum Exp m z experimental molecular ion m z of the best matching spectrum for this compound Delta m z m z difference between the value in the best matching spectrum and the corresponding value annotated for the reference spectrum Intensity Intensity associated with the best matching experimental spectrum d Identified Compounds The matching spectra For each identified compound The name of the compound is shown followed by a table that recalls information from the corresponding line in the Library Search Result table For the represented spectrum Score Exp RT Delta RT Exp m z Delta m z and Intensity are shown This is followed by a pair of spectra representing the corresponding experimental spectrum on top and its best matching reference spectrum on bottom for each MSn level The respective spectrum titles are displayed and information on experimental and reference MS level and polarity is shown 2 Full PDF This report displays the list of the identified chemical compounds a representative chromatogram and spectral match details for ALL matching spectra per compound for a given analysis It is the report named Full PDF in the results page The first 3 sections are the same as in the Standard PDF report The last section Identi
5. on the check box and validate on the apply button to display all unidentified spectra on the chromatogram These are highlighted as grey spots behind the chromatogram trace Filters M m z 0 4 Da RT min now unidentified spectra gt apply x reset ue 4 1 0e 8 Experimental sgectrum selected ee 8 0e 7 F spectrum 3 6 0e 7 0 2 a grey spots for f beta bh bind sila d vi 4 0e 7 unidentified no identification pre ee spots 0 0e 16 ao 2 4 6 8 10 12 14 0 20 40 60 80 100120 140 160 180 200 O 240 260 280 300 320 Retention Time min m z Da e ao Chemical compound Hits Score Delta RT Exp m z Ref m z Delta m z Ref E Info Aldiiineslnatekes unidentified Desipramine amp 3 0 90 8 74 267 2000 267 1856 0 0144 2 2 Experimental spectrum Referencdtbection Diazepam 0 90 9 75 285 1000 285 0790 0 0210 2 2 Spectumname TITLE 194 no Reference Olanzapine e 6 0 90 4 08 313 1000 313 1482 0 0482 2 2 Molecularionm z 328 2000 spectrum Zolpidem O 3 0 89 6 63 308 2000 308 1758 0 0242 2 2 Precursorm z 328 2000 D4 Haloperidol B 7 0 88 8 25 380 1000 380 0074 0 0926 2 2 Retention time 7 65 Cocaine 3 0 87 6 48 304 1000 304 1544 0 0544 2 2 Polarity Metamphetamine B 9 0 83 5 22 150 1000 150 1278 0 0278 2 2 MSlevel 2 Paracetamol 2 0 80 1 47 152 0000 152 0707 0 0707 2 2 Intensity 5 5951188E7 Venlafaxine amp 1 0 30 0 14 278 2000 278 0000 0 2000 2 2 Chemical compound CAS Synony
6. submitted Status Status of the analysis Owner name of the user who submitted the analysis only available for admin users Display hide analyses Hide analyses from the list Select one or more analyses use the checkbox and choose hide in the Action drop down menu to remove them from the list Show hidden Click on the show hidden check box to display all analyses Unhide analyses Once the Show hidden check box is activated you can select one or more analyses and choose unhide in the Action drop down menu to let them reappear in the list You can choose how many analyses you wish to see displayed per page SENEBIO v er name demo user a 4 Exit 6 S m a MS Analysis rl Library al Administration Help Refresh Analysis list PDF spectra Description Date uploaded Status aSET1 U 022 Dilutior A 380 DataSET1 U_14_0022 _Dilution_5 2010 07 12 oe unhide aSET1 U_14_0022 ilutior A 386 DataSET1 U_14_0022 _Dilution_10 2010 07 12 310 DataSET1 U14_0022_Dilution DataSET1 CheckMix 2010 07 12 w o ra ataSET1 MeOH 2010 07 12 D Action menu 1382 R esubmission Gob 307 2010 07 12 DataSET1 MeOH mzXML LJ v NTS Selection checkbox b e eeo Select how many analyses to display Eaa Next Jobs 1 to 200 Number of analyses displayed per page 200 Search analyses search Search analyses The search functionality allows you to restrict the
7. submitted analysis Sample Description spectra number of considered individual spectra SmileMS user manual 31 v1 2 May2011 b Information about the submission criteria and the reporting filters Profile Name name of the submission profile Library name of the library libraries queried Score threshold Min peak matches Prec tolerance Da m z tolerance on the molecular ion as set in the profile RT tolerance min retention time tolerance as set in the profile MS level filter as set in the profile Polarity filter as set in the profile Report m z filter Da m z tolerance on the molecular ion as set in the result page Report RT filter min retention time tolerance as set in the result page Report MS level filter as set in the result page Report Polarity filter as set in the result page b A chromatogram annotated with the positions of the identified compounds the identified compounds are represented with an index number and placed at the position of the best matching spectra c The Library Search Result The list of the identified compounds This table displays each compound in one line The columns are index number this number is used to find the compounds on the chromatogram Chemical Compound name of the compound as stored in the library Score the best matching score for this compound Hits number of individual spectra matching this compound Exp RT experimental retention time in minutes
8. the vertical bar with a on the far right part of the page The spectrum viewer contains three elements The spectrum match graph The spectrum match annotation info tab The Additional matches tab SmileMS user manual 21 v1 2 May2011 name admin admin SENEBIO s Exit 6 Sm i e MS Analysis Fl Library Administration j Q Help 2 Analysis list 3 Id 3 Filename small mix Ixq mzXML Description example Thermo LXQ Profile demo profile Date 2010 09 28 Filters Y m 2 0 4 Da a lel RT min Polarity MSlevel Show unidentified spectra gt apply x reset Fa Chromatogram reset zoom reset zoom 4 0e 5 i Experimental spectrum 3 0e 5 2 0e 5 NSUBJUT 1 0e 5 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 0 100 200 300 400 Retention Time min m z Da Chemical compound Hits Score Delta RT Exp m z Ref m z Deltam z Ref Exp Info Aiton patches Experimental spectrum Reference spectrum D4 Haloperidol 10 0 91 14 04 380 4000 380 4000 0 0000 2 2 Spectrum name 1833 Flecainide Paroxetine 6 0 91 13 81 330 2000 330 2000 0 0000 2 2 Molecular ion m z 415 1500 415 2000 Sotalol 10 0 91 5 96 273 1000 273 1000 0 0000 2 2 Precursor m z 415 1500 415 2000 D3 Chlorpromazine 14 0 90 16 24 322 1500 322 2000 0 0500 2 2 Retention time 14 57 0 00 Hydrocortisone 3 0 89 7 74 363 2000 363 2000 0 0000 2 2 Polarity Zolpidem 42 0 88 3 84 308 2500 308 2000 0
9. the y axis scale to the full Chromatogram range Chromatogram of A reset zoom Y rescale spectrum viewer 4 0e 5 3 0e 5 Y rescale button up original full unzoom y scaling 2 08 5 ASUS JUIT 1 08 5 0e 16 13 14 15 16 17 18 Retentian Time min Show unidentified spectra select the corresponding check box and click on the apply button to display all fragmentation spectra acquired in the analysis They will be shown as grey spots SmileMS user manual 25 v1 2 May2011 Filters W m z 0 8 Da MIRT 0 5 min how unidentified spectra gt apply x reset wen reset zoom rescale spectrum viewer Chromatogram of 1 2e 5 unidentified spectra are displayed as grey spots 1 0e 5 2 0e 4 ABS US BUT 6 0e 4 4 0e 4 2 0e 4 O 0 16 13 14 15 16 17 18 Retention Time min he note The chromatogram is created from the information available in the extracted peaklist files Each point of the chromatogram represents one MSMS scan The time of the acquisition is on the x axis and the associated intensity is either the intensity of the precursor ion in the respective precursor spectrum or the TIC of the actual scan Therefore the chromatogram can be very similar or very different to a MS1TIC or BPC depending on the acquisition conditions criteria and information delivered in the extracted peaklist file The Spectrum viewer To open close the spectru
10. to the Administration gt Profile manager section and either create a new Profile that searched this library or replace add this library to an existing profile See more details in the Profile manager section in the Administration page chapter below SmileMS user manual 38 v1 2 May2011 Install a NIST binary formatted library This section describes how to convert a library in a NIST binary format into a SmileMS readable format and to install this library in SmileMS Prerequisites The prerequisites for the procedure are A SmileMS server already installed lib2nist exe application that is part of the NIST MSSEARCH software package Overview of the procedure The update procedure consists in Convert a library from a NIST binary format to a SDF format Import this converted library to SmileMS Add this library to a submission profile The procedure Convert the NIST binary formatted library to a SDF format 1 Open ib2nist exe The program is by default in C Program Files NISTMS MSSEARCH directory 2 Select the library to convert click Open Convert MS Libraries or Datafiles to NIST or HP JCAMP Format BAH MISTES Input MS Library or Datafile Outpl Drives Path C C Program Files NISTM SSMS SEARCH E mM TEXT SAMP MSP EH MS2MSSM53 wh pol switch SOF ESH pist_mems SOF En STRUSAM SDF P STRUSAMP SDF mm COCZJNE MSP yy nisk mem
11. 0500 2 2 MSlevel 2 2 Intensity 1355 583251953125 1 0 Chemical compound Flecainide CAS 54143 55 4 Synonyms N Piperidin 2 ylmeth Library small demo edit edit Show compound in PubChem Evaluate a result The Table of matched chemical compounds The list of identified molecules is available in the Table of matched chemical compounds Each molecule is represented with its Chemical compound name a colored label to situate it on the Chromatogram the number of experimental spectra matching this compound ff Hits Additional columns display information on the best matching spectrum the Score the experimental retention time Exp RT the retention time of the corresponding spectrum in the library Ref RT the retention time difference between Exp RT and Ref RT Delta RT the experimental molecular ion m z Exp m z the molecular ion m z of the corresponding spectrum in the library Ref m z the m z difference between Exp m z and Ref m z Delta RT The polarity and MS level for both reference and experimental spectra Ref Exp A few columns are hidden when the spectrum viewer is displayed 2 3 means that Ref spectrum is a positive MS2 and Exp is a positive MS3 SmileMS user manual 22 v1 2 May2011 As a Chemical compound can be identified with more than one spectra Hits gt 1 click on the button to view details on all matching spectra for the selected
12. 14_small_mix_qrap3200 mezXML Profie Name demo profile Prec tolerance Daj 04000 3 2 RT tolerance min 100 ME level ffer OFF 4 0 90 968 a74 267 2000 00144 LERET Potarty fter oF Score threstoit os Min 8 peak matches 1 Library smal semo Sampie O 3 dt buske Compound Desipramine Spectrum 1 Tite Desipramine Score 0 90 RT 9 68 min Exp Ref MS levet 2 2 Exp Ref polarity Expartnantal Spectrum 4 1 Chromatogram 100 6 76 am eaj sepa 100 000 000 coisas ae HEE SS E z 3 A E i oat e i i i 00 a i 4 la i n 75 000 000 60 76 100 128 160 175 200 226 250 5 F ne E 50 000 000 Reference Spectum Desisramine 2 100 25 000 000 f 3 r a A z 1 0 76 gt f PA EEE ee Se AE E AR i PM 1 BRS TS ee ER eto 1 0 1 2 3 4 5 6 T amp 9 10 11 12 13 14 15 16 E Retention Time min en 2 Library Search Result en nal A nl a I POTEN N l 60 76 100 125 160 175 200 226 250 276 aaa ne i m rere 267 2000 565 1000 1000 n 308 2000 380 1000 304 1000 r 5 Metarretretarra 83 600 1000 00278 740000 00 Compound Dlazepam Paracetamol 80 s2000 00707 293330 31 Spectrum 1 Tite Diazepam Score 0 90 RT 10 90 min Exp Ref MS level 2 2 Exp Ref polarity raare 30 78 2000 02000 873333 31 gt p Exparinemal Spocium 225 109 7 4 ns 0 76 00 oat sw NER i ILA akh bth 6 70 BD S 300 110 128 120 168 950 168 170 180 150 200 20 220 238 240 260 260 270 280 290 308 310 ne EmieM3 Geneb
13. 56 9 823633333333333 Nordiazepam 270 8730 270 8730 5 37 Polarity MS level 2 2 Intensity 6673333 0 1 0 Chemical compound Nordiazepam Nordiazepam CAS 1088 11 5 Synonyms Library small demo X bruker amazon cancel add edit Show compound in PubChem Once you have finished the edition click on the save button The information will come back to the original information and a popup windows tells you that the edited spectrum is saved in the selected library Do If you want to add a spectrum to a new library you have first to create an empty library in the library management and then add the spectrum to this newly created library Wote The fields CAS and Synonyms are associated with a chemical compound and can only be edited in the library details view page To modify the annotation of a library spectrum functionality restricted to admin users Click on the edit button at the bottom of the Reference spectrum column The editable fields are displayed in individual boxes These are pre filled with information related to the spectrum and the associated compound Some values are rounded in the normal display such as molecular ion m z precursor m z Retention time Intensity The complete value is visible in edit mode You can decide to change the information adjust the molecular ion adapt the Retention time to new chromatographic conditions Info Additional matches Experimental spectrum Reference spectru
14. 6ENEBIO SmileMS GENEVA BIOINFORMATICS GENEBIO SA SmileMS documentation SmileMS user manual v1 2 May 2011 SmileMS user manual Geneva Bioinformatics GeneBio SA Av de Champel 25 CH 1206 Geneva Phone 41 22 702 99 00 e Fax 41 22 702 99 99 Email smilems genebio com Web www smilems com SmileMS user manual v1 1 December 2010 Table of Contents Introduction to the user MANUAI cccccceeeeeeeeeeeeeeeeeees 4 INO ESS Eee er seere 5 USE el Ce ia mr beet acetates needed ae ser eee banes 6 Whati SmileMS geno messer ele Do see Ed 6 How to cite SMIIEMS oo eee renerne renere ere rener en ere 7 Systems REQUIFEMENMS c ccccceeeeeeeeteeeeceeeteeeteeeeaeeetes 7 SmileMS installation cece eee eeseeseeeeeseeeeesaeeeeeeeeaees 8 Install the SmileMS server and raw data module ccue 8 Restart the SmileMS server X Gu X uvssseeeeeeeeereee renerne nerne r kernen rer 10 COnnguraton SetiNg Senni ee tees tated tee eet ies 10 Optional settings for the installation of the SmileMS server 10 How to change the memory to allocate to SmileMS ceeeeeeee 10 Network proxy firewall issues ccccsecceceeceeseeeeeeeeeeseeeeseaeeeseeeess 10 What is installed by the SmileMS server installer 11 What is installed by the SmileMS raw data module 11 What else needs to be installed to work with SmileMS 11 How to uninsta
15. Inc Firefox is a trademark of Mozilla Foundation Xcalibur is a trademark of Thermo Fisher Scientific Inc Analyst is a trademark of AB SCIEXPte Ltd MassLynx is a trademark of Waters Corp SmileMS user manual 5 v1 2 May2011 User manual What is SmileMS Mass spectrometry is a recognized powerful analytical technique used to screen and identify a wide range of chemical compounds It is used routinely in many laboratories in fields such as Laboratory Medicine Forensic Toxicology Doping Control Food Testing and Metabolomics research The rapid introduction of LC MS and LC MSMS provides access to an extended range of molecules complementing the well established GC MS methods Current identification methods for both targeted and unknown screening increasingly rely on MSMS spectra library searches A number of challenges are however still to be addressed Fragmentation spectra of a given compound can vary a lot depending on the selected instrument and acquisition method Currently available MSMS spectral libraries do only cover a subset of these experimental conditions for the available molecules Algorithms offered in dedicated software solutions originate from the GC MS development and do not show appropriate performances for LC MSMS data In addition as this method is entering routine applications there is a need for a robust easy to use MS vendor independent and integrated solution for rapid screening of large sets of molec
16. aSET1 checkmix mzXML 389 DataSET1 checkmix _ 49 DataSET1i 230109 mzXML PA 380 DataSET1 230109 Date uploaded Status 2010 06 16 oe 2010 06 16 eo 2010 06 16 oe Date uploaded Status 2010 06 16 v 2010 06 16 oe 2010 06 16 wo The status is refreshed regularly every 2 minutes Click on the Refresh button to refresh manually Analysis list Action LI Show hidden gt new analysis j Generate a pdf report from an analysis J From the Analysis list page browse for the analysis of interest and click on the pdf icon to generate and export a pdf report Id v File name PDF spectra Description J 5i DataSET1 meohi mzXML A 345 DataSET1 meoh1 50 DataSETi checkmix mzXML A 383 DataSET1 checkmix 49 DataSET1 230109 mzXML 30 DataSET1 230109 The pdf report is divided into 4 sections A description of the analysis the search criteria and the reporting filters A chromatogram annotated with the positions of the identified compounds The Library Search Result The list of the identified compounds Identified Compounds The matching spectra Date uploaded Status 2010 06 16 e 2010 06 16 oe 2010 06 16 SmileMS user manual 17 v1 2 May2011 SmileMS Analysis Report 3 Identified Compounds Repon msz finer Da o4 Repon RT fiter min 1 0 epon MS level Mer Regon potarity ter FF sll Jeu D Duto 3010 0 9 Chemical Compound 1 Desipramine amp pera 389 File Name 12866838642
17. ady successfully introduced in Clinical and Forensic Toxicology as well as Food Testing Its extension to other fields of Laboratory Medicine Environmental Pharmaceutical and Metabolomics is therefore independent from the tool itself SmileMS is developed by GeneBio in collaboration with the Swiss Institute of Bioinformatics and the Department of Laboratory Medicine of the Geneva University Hospital in Switzerland How to cite SmileMS The algorithm imbedded into SmileMS has been published This publication can be used to cite SmileMS SmileMS Geneva Bioinformatics S A Roman Mylonas Yann Mauron Alexandre Masselot Pierre Alain Binz Nicolas Budin Marc Fathi V ronique Viette Denis F Hochstrasser and Frederique Lisacek X Rank A robust algorithm for small molecule identification using tandem mass spectrometry Analytical Chem 2009 Sep 15 81 18 7604 10 Systems Requirements SmileMS is a client server application Here are the prerequisite requirements for a SmileMS server Intel Dual Core CPU 4GB RAM 1 5GB disk space for installation For optimum use of SmileMS allow at least 300GB Windows XP SP2 or SP3 Windows Vista Windows 7 32 bits version Adobe Acrobat reader The SmileMS Graphical User Interface is a web based interface You will access it using a web browser Supported web browsers are Firefox 3 5 0 and later with Flash Player version 10 installed Internet Explorer 7 and later with Flash P
18. age unzip the SmileMS installation package zip file in a local directory open the index html file in Internet Explorer To do so right click on the index html file select Open With and choose Internet Explorer mus To install SmileMS you need to log in Windows with a user that has administrative rights on the computer LS note The raw data processing environment uses the open source Proteowizard www proteowizard org tool to extract peaklists from various vendors raw data files This software is packaged in an installer made available for free to facilitate its installation For Thermo users the installation require to set windows Regional Settings to English United States Please see the installation instructions for more details ice If you are using a Windows installation using non Latin characters you need to make sure that your Windows regional settings are set to English United States before the installation process is started SmileMS requires appropriate number formatting and specific regional settings to work properly SmileMS user manual 8 v1 2 May2011 In Windows XP Go to Start gt Control Panel gt Regional and Language Options In the Regional Options tab select English United States Go then to the Advanced tab Select Apply all settings to the current user and to the default use profile Click OK 1 Go to gt g Control Panel gt w tegional and Language Options 2 Select a region that de
19. al interface is developed using the Flash technology you need this browser to have an Adobe Flash Player installed If it is not installed you will be asked to install it via a hyperlink You can get it from http get adobe com flashplayer As SmileMS can generate reports in pdf format you need to have a pdf reader to view them for instance Adobe Acrobat Reader SmileMS user manual 11 v1 2 May2011 How to uninstall SmileMS Go to Start gt Control Panel double click on the Add and Remove Programs icon select SmileMS and remove the installation W oeme uninstall procedure will erase the data folder If you wish to keep the data ask us how to do a backup of SmileMS content The uninstall procedure will also remove the proteowizard installation To uninstall the other modules go to Start gt Control panel double click on the Add and Remove Programs icon select the modules and remove the installation Be aware that some of these modules might be used by other applications already on your computer and were installed prior to SmileMS installation Removing them may cause other programs stop working About SmileMS user types SmileMS allows two types of users who are allocated different rights and privileges Admin has the maximum rights They can see results from all other users they can administrate profiles users and libraries etc User has restricted rights For example they cannot see jobs from other users t
20. ary matching Zolpidem only Right a bad match lower score best match two conflicting molecules Using the filters bar Functions available on the bar above the chromatogram and spectrum viewer can be used to manipulate a result i e to increase decrease the tolerances applied to precursor m z and RT windows as well as browsing through unidentified spectra Typically this may help to identify low scoring molecules adducts metabolites of molecules in the library and add new spectra ina library Filters W m z 0 4 Da RT min Polarity MS level Show unidentified spectra gt apply x reset The m z RT Polarity and MS level filters These filters can increase or decrease the stringency of the result By default the values displayed for these filters are those of the submission profile You can change these values Click on apply to activate the function Unchecking the check boxes will inactivate the corresponding filters Comment a negative filter value is equivalent to an inactive filter Bis m z RT Polarity and MS level filters functionality is available to admin users only Regular users cannot change these values For them the checkboxes are not available and the values are displayed in a grey background SmileMS user manual 29 v1 2 May2011 Filters mz Da min Polarity MS level Show unidentified spectra gt apply x reset The Show unidentified spectra functionality Click
21. ated with a spectrum Spectrum name Molecular ion m z Precursor m z Retention time min MS level Polarity However information such as Chemical compound CAS number and Synonyms is associated with a chemical compound Therefore when one of these fields is edited this is reported to all spectra belonging to the same Chemical compound Export a library You can export the list of compounds and the number of associated spectra in pdf format From the library tab click on the pdf icon You can export a complete library in SmileMS xml format Click on the Export button This functionality is restricted to admin users SmileMS user manual 35 v1 2 May2011 Upload create a new library As user with admin privileges you can import a spectrum library into SmileMS or create a new empty library and add manually spectra to it he Note To search this newly installed library don t forget to associate it with a profile See the section Search the newly installed library at the end of this section In the Library list window click on the new library button to prepare for the installation of a new library A pop up window appears for you to enter a Name and a Description While creating a library you can choose to add spectra to this library by importing data from a library file or to create an empty library and then add spectra manually from the result pages If you want to create an empty library select no New library Mame small
22. compound This will expand the compound with additional lines one per matching spectrum Click on the button to hide the details Some columns of the table can be sorted Click on the column title to sort them Le Note SmileMS calculates a score based solely on spectrum comparison Its calculation is based on a log likelihood ratio which means that it estimates the probability that a spectral match is not random false Filters such as molecular ion m z tolerance and Retention time tolerance are applied as post processing to the score calculation The scores in SmileMS range from 0 to 1 1 is the highest value These score values represent quality of match and are related to probabilities of being correct Acceptable thresholds for high quality matches may vary depending on the instrument instrument acquisition parameters library content and your own stringency acceptance levels According to the SmileMS algorithm that calculates probabilities of correct matches compounds displaying only a few signals 3 peaks or less might never get a high score as the intrinsic chance of matching a random spectrum is increased compared to a richer spectrum and thus the probability of being wrong is increased based solely on the spectral matching Therefore applying molecular ion m z filter and RT filter can be useful to validate those more difficult compounds The Chromatogram The Chromatogram displays MS or MSMS signal intensity as functio
23. creen_BP testAB pab test export impor Update 15 Edit the information Drag the library libraries to be searched from the Available library to the Selected library boxes 16 Click on Update The submission profile is available from the new analysis function Administration page Users The user management system is the part of the administration workspace that allows to List existing users Update user definitions Password First name Last name Email address Default format Default profile Add new users SmileMS user manual 42 v1 2 May2011 name admin admin SENEBIO i F r Exit 16 Sm j I Z MS Analysis Library Administration Profile manager User Server configuration License configuration z User information admin demo Username Georges Email address georges morris com Default format AB SCIEX v Admin rights Wote Users can define a default format This is the data format that is by default selected when starting a new analysis from the Analysis list page Peaklist AB Sciex Agilent Bruker Thermo Waters iore Users can define a default profile This is the profile that is by default selected when starting a new analysis from the Analysis list page Default profiles are used in various integration processes Typically they are used to ensure the use of a unique profile throughout technicians of a laboratory Woe administrator
24. e universality of SmileMS offers the possibility to handle data from different instruments and vendors with one software Spectral libraries from various sources can be searched and you can build your own For any further information or help please contact us at smilems genebio com SmileMS user manual 4 v1 2 May2011 Notices SmileMS is developed by Geneva Bioinformatics GeneBio SA All intellectual property rights on SmileMS belong to GeneBio Copyright 2010 GeneBio All rights reserved GeneBio 25 Avenue de Champel CH 1206 Geneva Switzerland SmileMS uses a number of following third parties software including ProteoWizard Copyright CAMM Open Source Software for Rapid Proteomics Tools Development Darren Kessner Matt Chambers Robert Burke David Agus ParagMallick Bioinformatics 2008 doi 10 1093 bioinformatics btn323 Tomcat Software developed by the Apache Software Foundation http www apache org Copyright 1999 2010 The Apache Software Foundation All rights reserved Flex Copyright 2010 Adobe Systems Incorporated All rights reserved Postgres Copyright 1996 2010 PostgreSQL Global Development Group Spring Copyright 2010 http www springsource org Other Copyright or trademark notices for products mentioned in this document Windows is a trademark of Microsoft AdobeAcrobat Reader is a trademark of Adobe Systems Inc Adobe Flash Player is a trademark of Adobe Systems
25. ental gpecttum Reference spectrum 0 91 14 19 415 2000 415 2000 0 0000 2 2 Spectrum name TITLE 1833 Flecainide 0 91 14 02 415 1500 415 2000 0 0500 2 2 Precursor m z 415 1500 415 2000 1 91 14 1 415 1500 415 2000 O C 2 2 Retention time 14 57 0 00 91 14 415 2000 415 2000 2 2 i 2 Corresponding match 91 14 415 2000 41 2 2 level 2 93 a4 4153 1500 44 yt Intensity 1355 583251953125 1 0 TM sack eE AEAN eee Chemical compound Flecainide 91 14 415 1500 415 2000 0 0500 2 2 1 9 i CAS 91 14 415 1500 415 2000 0 0500 2 2 Synonyms 90 14 415 2000 415 2000 0 0000 2 2 Library dem Oo 1 415 151 415 2000 2 2 edit edit 14 415 1 41 2 2 s 14 415 150 415 2000 0 0500 2 2 Show compound in PubChem 14 41 415 2000 4i 0000 2 2 Zoom activate the zoom function magnifier button Drag over the region you want to zoom in Double click on an empty region or click on reset zoom to zoom out to original Chromatogram SmileMS user manual 24 v1 2 May2011 Chromatogram 4 0e 5 3 0e 5 2 0e 5 AP SUBIUT 1 0e 5 0 0e 16 _ F a a 2 4 6 g 10 12 i4 16 18 20 22 24 26 28 30 Retention Time min 1 2e 5 1 02 5 2 0e 4 AHEUBJUT 6 0e 4 4 0e 4 2 0e 4 0 0e 16 Retention Time min The Y rescale button when active default allows automatic rescaling of the Y axis of the zoomed Chromatogram at all magnified states to the max y value of the current zoomed in region Inactivate it to leave
26. er Processing raw data requires uploading one or more files depending on the vendor format AB SCIEX a pair of wiff and wiff scan Agilent all files in the AcqData subdirectory of a d directory Bruker xml peaklist file as generated by Data Analysis Thermo raw file Waters all files in a raw directory em About AB SCIEX multi samples wiff files One AB SCIEX wiff file can contain multiple MS acquisitions different runs controls washing steps etc When you SmileMS user manual 15 v1 2 May2011 have uploaded a pair of wiff and wiff scan files that contain multiple samples a new pop up window appears that lists the samples You can choose what sample s you really want to submit to SmileMS via the check boxes The SmileMS analyses descriptions are pre filled with the original wiff filename and the samples descriptionsare entered as Analyst You can change these descriptions before confirming which analyses to submit to the identification process Extracted sample s Description DataSET1 MeOH 2 DataSET1 MeOH 3 DataSET1 MeOH 4 BEE I DataSET1 MeOH 5 K DataSET1 MeOH K DataSET1 CheckMix K DataSET1 U_14_0022 _Dilution_10 K DataSET1 U_14_0022 _Dilution_5 Select all Unselect all gt submit x cance I he note In cases you are submitting many jobs in a row it might happen that the profile drop down menu does not contain any
27. fied Compounds includes not only one spectral pair per compound for each MsSn level but all pairs of spectra identifying the listed compounds The tables in the Identified Compounds section include as many lines as there are experimental spectra matching the corresponding compound for each of them there is a graphical representation of a matching pair This report can be very large and may take several minutes to generate SmileMS user manual 32 v1 2 May2011 3 Identified Compounds Chemical Compound 1 Desipramine Spectrum Score Exp RT Delta RT Exp m z Delta m z Intensity 1 0 90 9 68 8 74 267 2000 0 0144 4446666 50 2 0 85 9 70 8 75 267 2000 0 0144 3633333 25 3 0 76 9 73 8 75 267 2000 0 0144 1320000 00 Visualize modify export and create spectra libraries The Library workspace allows you to install new libraries to visualize the content of a library compounds spectra spectra annotation to modify the content of a library compound name spectra annotation and to export library contents name admin admin SENEBIO jr Exit f Sm j e MS Analysis 4 Library i Administration aN Help O Library list Fnew library Library Y Description compounds small demo small demo library from different instruments 21 pabtest 1 Pesticides AB Sciex 547 NISTOS nist msms 08 2972 Open a library In the Library list page the list of installed libraries is shown in a table format Each installed library i
28. fines a dot 3 In the Advanced tab select Apply all as unit separator settings and click OK Regional and Language Options Regional and Language Options Regional Options Languages Language for norn Unicode progral Regional Options Languages Advanced Standards and formats This option affects how some programs format numbers currencies dates and time Select an item to match its preferences or click Customize to choose This system setting enables non Unicode programs to display menus and dialogs in their native language It does not affect Unicode programs but it does apply to all users of this computer Select a language to match the language version of the non Unicode programs you want to use Eng sh United States English United States v Samples Number 123 456 789 00 2S 456 F 789 00 Currency 123 456 789 00 Time 3 rg 1000 Roman batalia C 10001 MAC Japanese Short date 7 12 2010 7 10002 MAC Traditional Chinese Big5 Monday July 12 2010 Goce ae C 10005 MAC Hebrew Code p ge conversion tables Location To help services provide you with local information such as news and weather select your present location irer Saren setings Apply all settings to the current user account and to the default Switzerland fer profile In Windows vista and seven it looks like this Go to Windows g
29. hey cannot change filter values in results they cannot create or modify profiles from other users and they cannot create or modify user profiles Start and log in to SmileMS There are two possibilities to start the SmileMS interface on a local computer 1 Start gt All Programs gt SmileMS gt SmileMS 2 Open your preferred browser and type the url http localhost 8081 smilems You will arrive at the login page Two users are predefined in SmileMS username demo no password with user privileges and username admin password admin with admin privileges Additional user names and passwords can be defined by admin users See the Administration section Dive If you want to log in from a remote computer ask IT for the IP address or the name of the SmileMS server Use then this info and replace localhost in the url for instance http my_smilems_server 8081 smilems Make also sure that the url is accessible you might have to ask IT to open the firewall for connections to the SmileMS server K rrousleshoot cannot login to SmileMS SmileMS user manual 12 v1 2 May2011 have no network connection and I m using Firefox If your computer is not connected to any network you are therefore running SmileMS on a standalone machine and you use FireFox as browser it may put itself in offline mode This means that you will not be able to connect to the SmileMS server from your browser To bypass this in Firefox select F
30. his functionality is searching via internet and is only available if you have access to Internet Admin users have access to edit buttons that allow to either add an Experimental Spectrum to a library or to modify the annotation for a Reference Spectrum Info Additional matches Experimental specbum Reference spectrum Spectrum name 384754 Periciazine Molecular ion m z 366 3963 366 1635 Precursor m z 366 3963 366 1635 Retention time 6 41 0 76 Polarity MS level 2 2 Intensity 173979 5 1 0 Chemical compound Periciazine CAS ZO27 26 6 Synonyms Library AB SCIES Forensic edit edit Show compound in PubChem To add an experimental spectrum to a library functionality restricted to admin users Click on the edit button at the bottom of the Experimental spectrum column The editable fields are displayed in individual boxes These are pre filled with information related to the spectrum Some values are rounded in the normal display such as molecular ion m z precursor m z Retention time Intensity The complete value is visible in edit mode The name of the corresponding compound is automatically filled You can select the name of an existing library where the experimental spectrum and its annotation will be saved SmileMS user manual 27 v1 2 May2011 Info Additional matches Spectrum name Molecular ion m z Precursor m z Retention time Experimental spectrum Reference spectrum 222 271 1000061035156 271 10000610351
31. how this minimum number of shared m z values 11 Libraries Select one or more libraries to be searched Drag and drop libraries from the Available library box to the Selected library box SmileMS user manual 44 v1 2 May2011 Name Description Shared profile Precursor tolerance Da Retention time tolerance min Polarity filter MS level filter Scaring Min score threshald Min of peak matches Libraries Edit a submission profile Pesticides HMA Ei E E High mass accuracy Oz o Available library small demo amazon Toxlib 800 AB Forensic test pab bek lg Update Activated kd 1 Activated J 7 Tolerance on fragments Da Selected library Pesticides 5600 Wists to select a library drag its name from the Available library list and drop it in the Selected library list Server Configuration The server configuration is the part of the administration workspace that allows setting server variables Default profile a default analysis profile for the server This profile will be used if a newly created user has no personal default profile Tolerance in high mass accuracy scoring Da the default tolerance value to consider to match peaks in fragmentation spectra for the High mass accuracy scoring SmileMS user manual 45 v1 2 May2011 Profile manager User Server configuration License configuration Server variables Default profile
32. ile and uncheck Work offline want to connect to SmileMS from remote computer neither Start gt All Programs gt SmileMS gt SmileMS nor http localhost 8081 smilems does work These connections are only valid for the computer where SmileMS is installed If you want to log in from a remote computer ask IT for the IP address or the name of the SmileMS server Use then this info and replace localhost in the url for instance http my_smilems_server 8081 smilems Make also sure that the url is accessible you might have to ask IT to open the firewall for connections to the SmileMS server get to the login page but cannot connect The Tomcat server may be off From the SmileMS computer go to Start gt All Programs gt SmileMS gt smstomcatw and click on the start button get the login page but cannot connect bis The smspostgres service may be off go to Start gt Control Panel gt Administration tools gt Services search the smspostgres service and click on the start link If it does not start reboot your computer get the login page but cannot connect ter run the SmileMS server with Panda as security software Check if the smspostgres service is on If not start it go to Start gt Control Panel gt Administration tools gt Services search the smspostgres service and click on the start link If it does not start check if you can start pgadmin exe start c Program Files SmileMS pgsql b
33. ile Name 2 Profile Description 3 Shared profile makes this profile visible to all users 4 Precursor tolerance Da this value limits scoring results to those having a precursor m z difference above this threshold This filter can be deactivated using the corresponding checkbox 5 Retention time tolerance min this value limits scoring results to those having a retention time difference above this threshold This filter can be deactivated using the corresponding checkbox 6 Polarity filter this value limits scoring results to those with experimental and corresponding spectra having the same polarity 7 MS level filter this value limits scoring results to those with experimental and corresponding spectra having the same MS level i e both MS2 both MS3 8 Scoring choose between a standard scoring that performs matching with low mass accuracy fragmentation spectra and a scoring that performs matching with a high mass accuracy filter for the fragmentation spectra The corresponding tolerance is given in Da The High mass accuracy tolerance can be defined in the server configuration tab of the Administration workspace 9 Min score threshold this value limits scoring results to those having a score above this threshold 10 Min of peaks matches this value set the minimal number of MS signals to be paired in a match between an experimental and a library spectrum This implies that the scoring engine only considers matches that s
34. ileMS log in as user with admin rights for instance the default admin user 8 Goto the Library workspace 9 Click on the button New library give a name a description and select yes to the question Do you want to import spectra from a library file SmileMS user manual 40 v1 2 May2011 New library Name my library Description this is my library Do you want to import s yes spectra from a library file p no Upload library file x cancel 10 Upload the newly created SDF file 11 Click on create The upload might take a few minutes to more than two hours depending on the format and the number of spectra in the library 12 At the end of the process a pop up window appears that provide the number of spectra imported for this library Add the library to a submission profile To search the library with SmileMS you need to associate it with a submission profile 13 Goto Administration gt Profile manager 14 click on the New profile button to create a new one or select an existing profile to edit it SmileMS user manual 41 v1 2 May2011 Name Description Precursor tolerance Da Retention time tolerance min Min score threshold Min of peak matches Shared profile Libraries Edit a submission profile my new profile search my new library 1 Activated v Activated 0 3 0 w Selected library Available library pab test Drug_S
35. in pgAdmin3 exe If you get a message such as could not locate libpq dil reinstall SmileMS uninstall reinstall Make sure you have backed up the SmileMS data before reinstalling SmileMS get a popup window with the following error message Server Error Request 0 Refresh the page using the browser refresh button SENEBIO SmileMS SmileMS Version 1 0 www smilems com 2010 Geneva Bioinformatics GeneBio SA All Rights Reserved License Agreemen t SmileMS user manual 13 v1 2 May2011 Once logged into SmileMS you arrive at the Analysis List section The Analysis workspace is one of the three workspaces offered by SmileMS You can switch between the Analysis the Library and the Administration workspace by clicking on the corresponding banner button From all pages you have information on the logged user name and user type in parentheses access to an exit log out button and a help button which links to the user manual in pdf format SENEBIO Sm i I e MS Analysis Library j Administration Start an analysis and get a pdf report You can start a new analysis and get a pdf report from the Analysis list page in the Analysis workspace Start an analysis Select the new analysis button i GENEBIO Sm j amp MS Analysis pt Library Pt Administration J Analysis list resubmit v Show hidden Id Y File name gt new ana lysis PDF spectra Description Date uploaded S
36. installed on a computer not connected to any network and you use FireFox as browser Firefox will put itself in offline mode This means you will not be able to connect to the SmileMS server from your browser To bypass this in Firefox select File and uncheck Work offline What is installed by the SmileMS server installer The SmileMS server installer installation process installs the following elements Java Runtime Environment 1 6 The SmileMS server itself Atomcat web server A postgresql database Information in the computer registry A SmileMS item in the list of programs available from the windows Start menu Start gt All Programs gt SmileMS It includes a link to SmileMS and a link to a SmileMS administration console labeled smstomcatw which is mainly used to start and stop SmileMS and to change its allocated memory What is installed by the SmileMS raw data module The installation of the SmileMS raw data processing environment includes the following elements if not already there Microsoft Windows Installer only necessary for Windows XP Microsoft NET Framework 3 5 Microsoft Visual C MSFileReader useful only for Thermo users Proteowizard package What else needs to be installed to work with SmileMS SmileMS is accessible via a web browser such as Firefox and Internet Explorer This has to be installed on the computer you are using to access SmileMS As the graphic
37. io C 2010 Printed on Wed Now 24 185811 CET 2010 Page 1 SmileMS Genebio C 2010 Printed on Wed Nov 24 185814 CET 2010 Page 2 For a more detailed description of the information displayed on the pdf report see the The pdf reports section The Analysis list page The analysis page is located in the Analysis workspace It is a central page where you can start a new analysis resubmit an analysis view and search the list and status of already submitted analyses ask to open one or more results What information is available for each analysis The Analysis page provides the list of analyses available to be reviewed by a user in a table A user with user privileges will see only the analyses he she has submitted A user with admin privileges will see all analyses You can sort the analyses by clicking on the corresponding column title Each analysis is represented in a line and annotated with the following information ld a unique identifier attributed to this analysis File name The name of the processed peaklist file submitted to SmileMS When the analysis is successfully completed click on the file name to open the result view in a new tab PDF a link to the pdf report for this analysis H spectra number of MSn MS2 MS3 experimental spectra considered in the identification process Description Description of the analysis SmileMS user manual 18 v1 2 May2011 Date uploaded Date when the analysis was
38. item when the submission window pops up This is due to the limited amount of connections to the SmileMS server allowed by your browser Please wait for a few seconds until the profile items appear in the profile drop down menu Bun Once the submit button is clicked SmileMS first extracts peaklists from raw data and then launches the identification in a second step The extraction step can take from few seconds to several minutes depending on the size of the data file the number of included fragmentation spectra and the number of stored individual samples Follow the status of an analysis When raw files are submitted spectra are first extracted from the vendor proprietary format before submission to the identification process This is visible as a progress bar in the Analysis list page Analysis list resubmit v Show hidden gt new ana lysis running 1 spectra extraction s Id vy File name PDF spectra Description Date uploaded Status Identification runs can have different progression statuses represented as a colored dot in the analysis list page SmileMS user manual 16 v1 2 May2011 pending orange running blue completed green failed red click on the red dot to see the error message Id v File name PDF spectra Description ia 51 50 DataSET1 checkmix im 27 DataSET1 230109 Id vy File name PDF spectra Description 5i DataSET1 meohi mzXML 345 DataSETi meohi _ 50 Dat
39. layer version 10 installed It is best displayed with a screen resolution of 1280x1024 he Note Your web browser will ask you to install Flash Player when opening SmileMS the first time unless Flash Player is already installed SmileMS user manual 7 v1 2 May2011 FA are Adobe Acrobat Reader can be downloaded from http get adobe com reader You do not need to install the optional Free McAfee Security Scan Plus SmileMS installation SmileMS is designed as client server architecture so that it can be installed as a standalone program on any PC or on a server for network access by multiple users Remote access is therefore possible via a standard Web browser giving users the freedom to launch analyses and review results from other locations e g office home etc Install the SmileMS server and raw data module The installation procedure of the full SmileMS environment implies the installation of the SmileMS server itself and installation of the raw data processing environment The latter installs the needed software that allows you to submit native files from various MS vendors The installation can be done from the installation CD or from the downloaded archive as follows From the installation CD insert the CD and follow the instructions from the index html file that you are required to open in Internet Explorer To do so right click on the index html file select Open With and choose Internet Explorer From a downloaded pack
40. list of displayed analyses to those matching the search criteria The search is applied to the Description and the File name fields Perform a resubmission You can select one analysis and decide to resubmit it on another library and or using different search stringencies As these criteria are defined in profiles a resubmission means apply a search on a dataset using another profile Select one and only one analysis choose resubmit from the Action drop down menu A pop up wind opens where you can choose to select a new profile and change the Description By default the proposed description is Resubmission job nn where nn is the analysis ID to be resubmitted SmileMS user manual 19 v1 2 May2011 Load Data Data Files s Profile AB Forensic Description Resubmission job 43 Click on Upload file and select one file in peaklist format mzs ML omogf sdf gt submit x cancel Evaluate a result Open a result general description of the result page elements Clicking on a result file name from the Analysis list page will open the result in a new tab The result page displayed by default contains the following elements Descriptive information about the analysis analysis identifier Id Submission Filename Analysis Description Selected submission Profile Submission Date Mouse over a description to read a long text long texts are cut to 255 characters Actions on the result Tolerance fi
41. lize modify export and create spectra libraries 33 SmileMS user manual v1 1 December 2010 Opena DIG Y cacaccantccrencatcndastatcsdeceatmanctatmdecsatccdeutatcdastatendeatates 33 WISUAIIZE IBAN ENUY si cxcdantcnctdentcoesdentceutcesddawidandcancavadexndantiand 33 Wodity AD REN Enty vec secret ered erates 34 EXPO GMD GARY d AENEA 35 Upload create a new IIDIPary cccccceececeeeeseeeeseeeeseeeeseeeesseeesees 36 Search the newly installed library cccccccesseeeseeeeeeaeeeeeeeeees 38 Install a NIST binary formatted library ccccccecseeeeeeeeeeeeeees 39 Fee CIS eS tient tacensti tas danas aoktehalam ere a GER ease tants 39 Overview Of the procedure cccccseeeeccecceeeeeeeeceeeeeeeeeesuaeseeeesesaaeeeess 39 The procedure Erna diced 39 Administration page cccccecceecseeeeeeceeeseeeaeeceeeseeeeeeeaess 42 WIS OMS aaoi a Acie ee 42 Prolls MANGE FS zonen ende tek ar een ER actuate pE ER Sek AE 43 SEER GONMQUIATION 5 inen a a arte tere 45 LICENSE COMIGUIALION arrene enedes 46 How to renew a license cesatrrcnctthencrsmctesnetircahesinetl seumdeomcenraiiidautalcend 47 Automate submission to SmileMS or integrate with their party software using the SmileMS submission module NEE ote eich P OA E AE E AEE E at pete aso ee E EE E AE 4 Backup restore SMIIOMS cc ceececeececeeeeeeeeeeeeeeees 48 How to Backup the content of SmileMS cc ceeeceeeeeeeeeee ees 48 The procedure t
42. ll SmileMS 0 ce ccc cece ecceeeeeeeeeeeeeeeeneaeeaeeees 12 About SmileMS user tyPe cccccseeeceeeeeeeeseeeaeeeees 12 Start and log in to SMIIOMS cece eeeeeeeeeeeeeeeeetenees 12 Start an analysis and get a pdf report 14 Stat am AN AN S Ssss ted sis ans seed aenay dca Semupddadenns ANN 14 Follow the status Of AN ANAlYSIS cccceeccseeeceeeeeeeeneeeseeeeeeeens 16 Generate a pdf report from an analysis ccceeeeceeeeeeeeeeeeees 17 TNC ANAIY SIS MIST DAGE iss orne less ss reen 18 What information is available for each analysis cc scccee 18 Display hide analyses scaleeiiacaadvanetiinivinvteeiatiteiiedtineuivas 19 Search AN AV SES veces ore eee AE onen 19 Perform a resubmMmission X u sssseeeeererereeee renere kernerne kerner renere 19 Evaluate a result W u u u u svssseeeeeeereerereer nere er kreere rr ennen enker 20 Open a result general description of the result page elements 20 EV alates FESTE oner E 22 The Table of matched chemical COMPOUNGCG scceeseeeeeeneeeees 22 Ther ChromaO Gran vaca sca tein Rn ei rare a ER erkendes 23 The Spectrum VICWEL cccccceesceccseeeeceeeseeeceeeeeseeeeeeseaueeessaeeeessaeees 26 Using the Mers DAM ses iena a nerne eee ene se aes 29 Generate reports from the results page cccccceeseeeeeeseeeeneeeeeeseees 30 The results pdf reports cccccccccsseeeeceeeeeeeeseeeseeeeeeeeeeeesseeeesaaeees 31 Visua
43. lters on molecular ion m z and elution time RT filters on Polarity and MS level Show unidentified spectra check box result pdf export icon Chromatogram Table of matched chemical compounds SmileMS user manual 20 v1 2 May2011 name admin admin Exit SENEBIO Lad Sm le MS Analysis Library Administration Hel A Analysis list 3 Id 3 Filename small_mix_Ixq mzXML Description example Thermo LXQ Profile demo profile Date 2010 09 28 Filters V m z 0 4 Da _JRT min Polarity MSlevel Show unidentified spectra gt apply x reset Th Chromatogram reset zoom spectrum viewer 4 0e 5 3 0e 5 2 0e 5 NSUBJUT 1 0e 5 0 0e 16 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 Retention Time min Chemical compound Hits Score Exp RT Ref RT Delta RT Exp m z Ref m z Delta m z Ref Exp Flecainide 8 33 0 91 14 57 0 00 14 57 415 1500 415 2000 0 0500 2 2 D4 Haloperidol 10 0 91 14 04 0 00 14 04 380 4000 380 4000 0 0000 2 2 Paroxetine L 6 0 91 13 81 0 00 13 81 330 2000 330 2000 0 0000 2 2 Sotalol 10 0 91 5 96 0 00 5 96 273 1000 273 1000 0 0000 2 2 D3 Chlorpromazine 14 0 90 16 24 0 00 16 24 322 1500 322 2000 0 0500 2 2 Hydrocortisone BS 3 0 89 7 74 0 00 7 74 363 2000 363 2000 0 0000 2 2 Zolpidem 42 0 88 9 84 0 00 9 84 308 2500 308 2000 0 0500 2 2 The spectrum viewer element can be displayed by clicking on the spectrum viewer button or
44. m Spectrum name 208 Quetiapine Molecular ion m z 384 2000 384 098 Precursor m z 384 2000 384 098 Retention time 8 35 4 36713333333333 Polarity MSlevel 2 2 Intensity 5 150932E7 1 0 Chemical compound Quetiapine CAS 111974 72 2 Synonyms Library bruker amazon edit cancel update Show compound in PubChem SmileMS user manual 28 v1 2 May2011 Once you have finished the edition click on the save button The information will come back to the original information and a popup window tells you that the edited spectrum is saved in the selected library BNG The fields CAS and Synonyms are associated with a chemical compound Be careful when changing this information as it will impact all other spectra associated with the same compound name in the library The Additional matches tab provides information on alternative interpretations for an experimental spectrum Alternative spectra are displayed with the Chemical compound name and matching score This indicates whether there is a unique interpretation of a given spectrum or if there are potentially conflicting interpretations Experimenta spectrum Experimenta spectrum 0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 m z Da Info Additional matches Info Additional matches Chemical compound Score Chemical compound Score Zolpidem 0 89 Clozapine 0 25 Zolpidem 0 69 Prazepam 0 22 Zolpidem 0 66 Zolpidem 0 41 Left A good match 3 spectra in the libr
45. m viewer click on the spectrum viewer button or on the vertical bar with the or buttons on the far right side of the page Once you have selected a spectrum match either clicking on a spot on the Chromatogram or on a line in the Table of matched chemical compounds you can see a head to tail representation of a spectrum match The experimental spectrum is shown on top and the reference spectrum from the library is shown on bottom X axis is a m z scale and y axis represent signal intensities with values normalized to 1 on both axes Functionalities of the spectrum graph Put your mouse over a peak to see its annotation Actual intensities are labeled Zoom in by dragging a region on the graph Use the Y rescale button to automatically rescale the y axis of the spectrum to local maximum value Double click on an empty region or click on reset zoom to zoom out to original graph SmileMS user manual 26 v1 2 May2011 Experimenta spectrum 73 13 170 33 1 Reference spectram m z Da The Info tab provides annotations to experimental and reference spectra such as Spectrum name Molecular ion m z Precursor m z Retention time in min Polarity MS level Chemical compound name Chemical Abstracts CAS Synonyms Source Library name A link to NCBI PubChem Compound database http pubchem ncbi nlm nih gov will search the database with the Chemical compound name and open the result in a new browser window T
46. me to your experimental conditions You can change information about a compound ina library if you are a user with admin privileges Click on the edit button make your changes in the editable fields Spectrum name Molecular ion m z Precursor m z Retention time in min Polarity MS level Chemical compound name Chemical Abstracts CAS Synonyms Source Library name and click on the save button to store the changes All future queries to this library will consider the new values SmileMS user manual 34 v1 2 May2011 0 8 0 6 0 4 0 2 OSSE SAALE Reference spectrum 1 0 8 0 6 0 4 0 2 0 Reference spectrum 140 o 20 40 60 80 100 120 140 160 180 o 20 40 60 80 100 120 160 180 m z Da m z Da Reference spectrum 120711 Reference spectrum 120711 Chemical compound Cocaine Chemical compound Cocaine Molecularion m z 304 1544 Molecular ion m z 304 1544 Precursor m z 304 1544 Precursor m z 304 1544 Retention time min 0 82 Retention time min 0 816 MS level 2 MS level 2 Polarity Polarity CAS 50 36 2 CAS 50 36 2 Synonyms Synonyms L J cancel delete paun JL Show compound in PubChem Show compound in PubChem As you can add multiple synonyms to a compound a dedicated pop up window opens when you select to edit the Synonyms field Edit synonyms methyl 1R 2R 3 58 3 t methylbenzoylecgonine Additem x cancel gt ok Wace Most of the annotations are associ
47. ms Library edit In the spectrum viewer the unidentified spectra are displayed with no reference spectra graph and annotation as there is no matching spectrum in the searched library for these An unidentified spectrum can be edited and added to a library functionality only available to admin users The mechanism is similar to the edit mode for identified spectra see above In the case of a spectrum that was not identified a replaces the name of the compound The column reference spectrum remains empty Info Additional matches Experimental spectrum Reference spectrum Spectrum name Molecular ion m z Precursor m z Retention time 101 318 29998779296875 318 29998779296875 10 723766666666668 Polarity MS level 2 Intensity 3 317315E7 Chemical compound CAS Synonyms Library small demo v add cancel Generate reports from the results page Click on the pdf icon on the filter bar to generate a report of the current result You have the choice between a standard report and a full report SmileMS user manual 30 v1 2 May2011 The standard report provides a header with general information about the analysis a chromatogram a table listing the identified compounds and corresponding Standard PDF information for the best matching spectra and for Full POF each of them the corresponding pair of experimental and matching spectra The full report contains the Same information as the
48. n of Retention time in minutes Identified spectra are labeled with colored spots Each spot corresponds to an individual fragmentation full scan spectrum Its color is associated with a Chemical compound as displayed in the Table of matched chemical compounds Functionalities of the Chromatogram The Chromatogram has two main interaction modes the browse mode and the zoom mode You can switch from one mode to the other by selecting the hand or the magnifier button on the respectively STA The default mode is the browse mode In the browse mode Gl place your mouse over a spot to open a pop up window with matching information SmileMS user manual 23 v1 2 May2011 Compound Zolpidem Score 69 Experimental RT min 9 79 Reference RT min 00 Experimental mrz 308 3100 Reference mz 308 2000 6 2 10 12 14 16 15 Retention Time min Click on a spot to enlarge all spots of that compound to add a square to that particular spot to show the corresponding match in the Table of matched chemical compounds and if the spectrum viewer is open to show the spectrum match details Experimental spectrum 3 0e 5 5 rf 3 p 210645 Selected spot lt 1 0e 5 0 0e 16 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 Retention Time min Chemical compound Hits Score Delta RT Exp m z Ref m z Deltam z Ref Ex Info EE MET EVO REE Te Flecainide e 33 0 91 14 19 415 2000 415 2000 0 0000 2 2 Experim
49. ntensities Version 1 1 26 Support for Windows Vista and Windows seven 32 bits SmileMS works with all Latin characters OS Backup restore procedure the functionality is available in the installation package Support of raw and processed data improved handle spectra without precursor m z with negative intensities with negative m z with no peaks Analysis and profiles added filters for polarity and msLevel Analysis list improved speed of job list if a lot of jobs available Analysis list improved search functionality PDF exports improved Time out better handled Library parsers more efficient and bug fixed Fixed double login required in some installations and after time out Automation of submission to SmileMS from Xcalibur software via the SmileMS submission module Version 1 1 Spectral and compound level parameters are extended Support for polarity precursor m z msLevel CAS numbers Synonyms Library parsers adapted Analysis list page added Owner column Analysis performances improved handling of memory during identification and library creation Results Table of compounds added a polarity msLevel column for both Ref and Exp spectra Results Additional matches tab fixed missing hits when m z filters inactive Library list and details pages improved Library possibility to delete a spectrum from a library Library opening details on a library is accelera
50. o backup SmileMS cccceeccceceeeeeeseeseeeeseeeeeeneeeees 48 What happens during a backup procedure cccseecceeeeeeeeeeeeees 48 How to Restore the content of SmileMS from a backup 48 The procedure to restore the content of a backup eeseeeee 48 What happens during a restore ProCeduUre cccceeeecceeeeeeeeeeeeeees 48 What s new release notes cece eceeeeceeeeceeeeceeeeeeess 49 VENSIOMIN 15 220 stactdcntdesedawstosiderideredecttesidesidesitevidesttesadertdesiossdenddeee 49 VEION Ws lite aaa TEDE 49 Va GION U2 ccnsatcoaeqaneceocutNedet FEER TER BRED RV TER dante FEER VENS EVER FIRER VET ER EINE RUIN 49 GIGI Wi O12 OA icctientiectdnclsexsieed NE SE TREE FE ENE e E 50 POC 10 20 6 wissen REST EEN EET EET EDER ERE ES EST EET SETT EEN ENE 50 FNC Mie cia hse se ee RESEN TE STEEN ES ee ee ee ae ccc ne 50 NOO cnda ERE ERE DEERE EDER usenet a ERNE TEENS SERRERERNERER 51 SmileMS user manual v1 1 December 2010 Introduction to the user manual elcome to the SmileMS user manual In this manual we will guide you through installing SmileMS and introduce you to its major functions The innovative robust algorithm allows you to identify molecules with the highest level of confidence The intuitive graphical interface helps you running analyses in a few clicks You can then go on to evaluate the results using several different views and easily generate a comprehensive report Th
51. o the installation instructions the computer hosting SmileMS must be restarted at the end of the installation process Moreover an additional restart is also sometimes required please restart your computer a second time if you fail to login SmileMS after the first restart Configuration settings Optional settings for the installation of the SmileMS server During the installation of the SmileMS server some of the configuration can be set manually data folder to specify where do you want to store the SmileMS data web server port proposed default port for the tomcat web server is 8081 database port proposed default port for the sql database is 5433 ee the SmileMS data folder can be changed and set to a directory accessible on a local disk or on a mounted disk It is independent to the SmileMS program folder and can be archived as such This is however not sufficient to create a restorable SmileMS backup To create a SmileMS full backup please see the corresponding chapter How to change the memory to allocate to SmileMS You need to define how much memory to allocate to SmileMS Go to Windows Menu Start gt All Programs gt SmileMS gt smstomcatw Click on the Stop button in the General tab Select the Java tab and you can increase the value in the Maximum memory pool The value should not exceed the RAM of your computer Note that Windows 32 bit cannot allocate more that 1300 MB to Java 1024MB is an appropria
52. s MSP Em SAMPLIB MSP i SY NON MSP Add Input Libraries Files SmileMS user manual 39 v1 2 May2011 3 Select the library in the Convert MS Libraries or Datafiles to NIST or HP JCAMP Format window make sure that the options include the following checkboxes Include synonyms Keep IDs unchanged MS MS spectra only gt Convert MS Libraries or Datafiles to NIST or HP JCAMP Format LER NIST Library CAPragram Files SMS TM SSMSSEARCH B Options El r mez Rounding in Input File OK Multiply mz in imported spectra by ok mz Cancel and round to the nearest integer Example CH2 n correction is 0 99868 i How to Produce Output Optional i A nclude Synonyms Add following berm to all mz before rounding Keep IDs unchanged Mi from chem Formula MS MS spectra only Add Input Libranes Files Convert 4 Select SDFile SDF as output format 5 Click on Convert Convert MS Libraries or Datafiles to NIST or HP JCAMP Format SHE NIST Library C Program FilesSAISTMS4MS SEARCH El Output C Program FilesSAIS TMS SMS SEARCH w m Input Libraries or Test Files r NIST MS User Libraries Pe ee N m m rr oe C Program Converting C Program Files WISTMSSMSSEAARCHMS2MS3M53 wh pol switch Cancel How to Produce Output I Output Format 6 The converted sdf file is located in the same directory as the source file Upload the converted library to SmileMS 7 In Sm
53. s can access all functions whereas standard users can only view and modify their own parameters Profiles manager The profiles manager is the part of the administration workspace that allows you to manage submission profiles A submission profile is a set of parameters that SmileMS uses to perform identification This includes for instance the library to search the tolerances to apply to molecular ion m z and retention times minimal score threshold The profile manager window allows to List and modify existing profiles Add new profiles SmileMS user manual 43 v1 2 May2011 SENEBIO Sm J E MS Analysis Library Administration Profile manager Name demo profile CURML Q New profile User Server configuration License configuration Description Score threshold Prec tolerance Da RT tolerance min Min peak matches submission parame ters ford 0 3 0 4 deactivated 1 CURML small lib 0 3 0 7 deactivated 0 AB Sciex Forensic 0 3 0 7 deactivated 1 0 3 0 8 deactivate 0 0 3 0 8 0 4 0 1 0 4 deactivated deactivated W ote administrators can see and edit all profiles whereas standard users can only edit their profiles They can however see and use their profile as well as shared profiles Click on the New profile button to create a new profile or click on an existing one to edit it When creating a new profile or modifying an existing one users can enter information regarding 1 Prof
54. s represented in a line with its Name its Description the number of chemical compounds and the number of spectra it contains Click on a library name to get more details about this library This opens a new tab labeled with the name of the library Visualize a library entry Once you have opened a library tab you can browse the content of the selected library The list of the chemical compounds is displayed in a table Each compound is represented in one line with its name and the number of spectra the library contains for that compound The list can be sorted by clicking on the Chemical compound column title To visualize more details about one compound click on a compound name The compound is expanded and one line per spectrum is displayed with Spectrum name molecular ion m z and MS Level Clicking on a spectrum name opens a spectrum viewer that displays the actual spectrum and additional annotation information such as Spectrum name Molecular ion m z Precursor m z Retention time in min Polarity MS level Chemical compound name Chemical SmileMS user manual 33 v1 2 May2011 Abstracts CAS Synonyms A link to NCBI PubChem Compound database http pubchem ncbi nim nih gov will search the database with the Chemical compound name and open the result in a new browser window This functionality is searching via internet and is only available if you have access to Internet Click on the PubChem link queries the NCBI PubChem Compound
55. sh 17 restore 50 resubmission 19 result page 20 Search analyses 19 Server configuration 47 Show unidentified spectra 30 spectra libraries 33 Spectrum viewer 26 Start SmileMS 12 Systems Requirements 7 Table of matched chemical compounds 23 uninstall SmileMS 12 Upload a library 36 user types 12 Users administration 42 v1 2 May2011
56. st page It is then ready to be visualized and to be added to a submission profile Bice SmileMS can read the following formats AB SCIEX clq format and Analyst mdb library Bruker library format NIST sdf when uploading a sdf file you will be prompted to choose between a regular NIST sdf format or a Maurer sdf format sdf format with specific fields to the Maurer LC MSMS library SmileMS XML library format Other formats can be converted into one of the above using export functions from your preferred Acquisition software or using the nist2lib exe program as available in the NIST MSSEARCH software package oe SmileMS does not query and therefore does not store MS1 spectra in its database Only spectra labeled with a MS level 2 or higher are imported in SmileMS K rrouiesroor The library installation never ends the screen remains for ever with the progress bar and does not pop up the finished window The installation is still running Some libraries might need long installation time up to 3 hours for NIST_MSMS depending on your computer Just wait longer You can alternatively also open the windows task manager and see if a postgres exe process is running The installation went out of memory Stop the smstomcatw service and increase the memory allocated to Java see section How to change memory Search the newly installed library In order to search the newly installed library it needs to be defined in a profile Go
57. standard one and adds detailed information about all matching spectra for each compound r The results pdf reports Here is a description of the information displayed in the pdf reports that can be generated from the Results page and from the Analysis list page Two types of PDF reports can be generated The Standard PDF and the Full PDF 1 Standard PDF This report displays the list of the identified chemical compounds a representative chromatogram and spectral match details for each best matching spectrum per compound and MS level for a given analysis It is the default report available from the Analysis page and the one named Standard PDF in the result page This report is a multi page report stored in an Adobe Acrobat PDF format It is divided into four sections a A description of the analysis the search criteria and the reporting filters b A chromatogram annotated with the positions of the identified compounds c The Library Search Result The list of the identified compounds d Identified Compounds The matching spectra the best matching spectral pair for each compound etern ree jer other spectra pages Further details of the four sections a A description of the analysis the search criteria and the reporting filters a Information about the Sample and submitted MS run SmileMS JobID Job ID in the SmileMS server File Name name of the converted MS run submitted to SmileMS Date of the
58. t How to renew a license You need to renew a SmileMS license to continue to use SmileMS after the trial period is expired or to install a permanent license if you have purchased SmileMS You need to contact GeneBio and provide your Host id You will receive an email that includes a license lic file Once you have received and saved your lic file on your computer simply click on Upload file and select your newly saved lic file This automatically renews your current SmileMS license Automate submission to SmileMS or integrate with their party software using the SmileMS submission module The SmileMS submission module is a separate piece of software that allows to a Perform submission to SmileMS in a command line mode b Configure an automatic submission to SmileMS at the end of a MS analysis on Thermo Fischer instruments via Xcalibur c Allow an integrated solution with Bruker amaZon instrument control This module interact with SmileMS via a web protocol and can be installed either on a computer where SmileMS is also installed on a computer that is remote and can access SmileMS via the web If you are interested to install and use the SmileMS submission module please contact us at smilems genebio com SmileMS user manual 47 v1 2 May2011 Backup restore SmileMS It is possible to backup the full content of SmileMS for archiving purposes and restore it later if needed How to Backup the content of SmileMS The procedure
59. t Control Panel then i 368 Ja Gu gt Cortrel Pane gt l j rJ go b Control Pane p Seow P Nare Category v rt Panel Home etol Panel horne System and Maimenance User ACCOUMS AN Fet Rated an Wetchows O Range aourt pe 2 Bock wg oma vw Appearance and Security h ae Personalization rock for update n we m wow Vert hange Secittop beckyround Ci i ses bange the y cheme dyrt screen reschbon Network and Internet E Vinee network states and tasks Clock Language and Region lt at up fie shanng pre rr uns orth gher rpa i Hardware and Sound Prey CDs Or other rede netomat l Ease of Access 4 r CODE gt Centre Panel Clock Language and Regien i Date and Time bet the tiene ond dete henge the tine tone hoch gedget to Widows fadet 9 Regional and Language Options EE 4 Change the country X henge HS h nge bete mE md meter Formats Lecaton Keyboards and Languages Admnaratve To change the way your computer displays mambers currencies dates and time select an entry from the format ist Examples of how data i displayed using this formet Number 123 456 789 00 123 456 789 00 14745 PM 12 7 2010 Tuesday December 07 2010 Custorme thes format Fer additional formats keyboards and tools go to the Microsoft mbar Ca Gem SmileMS user manual 9 v1 2 May2011 Restart the SmileMS server According t
60. tatus Previous Next Jobs 1 to 200 Number of analyses displayed per page 200 Search analyses search A pop up window opens Complete with the required information and click on submit The pop up window closes and you can follow the status of the analysis on the Analysis list page SmileMS user manual 14 v1 2 May2011 Load Data Format Peaklist v Upload file Click on Upload file and sel format mzXML mgf sml ect one file in peaklist sdf x cancel The submission pop up window asks you to 1 Select the file format from the Format drop down menu see also notes below 2 Click on Upload file to select the file s to upload see the text describing what file s is are needed and the notes below during the upload a progress bar appears next to the Upload file button 3 Select a submission profile from the Profile drop down menu see also notes below 4 Enter a description for the analysis this depends on the file format 5 Once all set click on submit Ci About file formats SmileMS directly processes peaklist files in various formats such as mzXML mgfand NIST sdf format Raw MS vendor specific datafiles are submitted to a spectrum extraction step prior to the submission to SmileMS This process uses the raw data module which is part of the SmileMS installation In addition Waters MassLynx data requires that MassLynx is installed on the same computer as the SmileMS serv
61. te value Click Apply then select the General tab again and click on the Start button Close the window Network proxy firewall issues SmileMS can work as a standalone application on one computer for instance a MS acquisition PC If you want to use SmileMS on a network configuration you may want to make sure remote computers can access the SmileMS server Depending on the network proxy and firewall settings on and around your SmileMS server please check the following if SmileMS does not start correctly If you are using a proxy define the access to SmileMS appropriately in all client browsers On your browser set the proxy detection to autodetect On Firefox go to Tools gt Options then select the Advanced option choose the Network tab Click on Settings and select Auto detect proxy settings for this network On Internet Explorer go to Tools gt Internet options then select the Connections tab click on the LAN settings button and check the Automatically SmileMS user manual 10 v1 2 May2011 detect settings option Another option is to add the SmileMS server url in the exclusion list of the browser proxy settings As some proxy definitions and constraints can be proxy configuration dependant ask your IT Server firewall Check the firewall installed on the SmileMS server Open the 8081 port or the port defined at the installation As this firewall might be defined in many ways ask your IT If SmileMS is
62. ted Library allow the creation of a library from a mzXMLL file Administration owner column added in Profile manager page Administration profile manager added checkboxes to activate inactivate RT and m z filters profiles with no library not allowed Administration possibility to define a default format and default profile for each user Administration fixed errors of license management PDF exports improved SmileMS user manual 49 v1 2 May2011 Patch 1 0 284 fixed AB SCIEX Analyst mdb formatted libraries having entries with no spectra failed to install Patch 1 0 283 fixed extended demo license demo sometimes not validated Patch 1 0 282 fixed bug for unsorted m z in mdb libraries fixed parsing of mzXML where intensities are in scientific writing SmileMS user manual 50 v1 2 May2011 Index Additional matches 29 Administration 14 Administration page 42 Analysis 14 Analysis list page 18 backup 50 Backup and restore SmileMS 49 50 Chromatogram 24 Configuration settings 10 Create a library 36 Export a library 35 file formats 15 filters 29 firewall 10 hide analyses 19 installation 8 Library 14 Library list 33 License configuration 48 m z and RT filters 29 memory 10 Modify a library entry 34 new analysis 14 SmileMS user manual 51 New analysis 14 new library 36 pdf report 17 31 Profiles manager 43 proxy 10 PubChem 34 Refre
63. to backup SmileMS On the SmileMS computer create a directory where you want to store a SmileMS backup Copy the content of the C Program Files SmileMS backup directory or where SmileMS is installed in this newly created directory Go to this directory and double click on the sms_backup bat file What happens during a backup procedure SmileMS is stopped a subdirectory is created the sms_restore bat script is copied in this subdirectory a dump of the SmileMS database is created and all of the data directories are also copied in this subdirectory Then SmileMS is started again How to Restore the content of SmileMS from a backup The procedure to restore the content of a backup Go to the directory containing a SmileMS backup Double click on the sms_restore bat file What happens during a restore procedure SmileMS is stopped all data libraries user definitions profiles etc from the active SmileMS are deleted and replaced by the information on the backup Then SmileMS is started again SmileMS user manual 48 v1 2 May2011 What s new release notes Here are summaries of new features and main corrections Version 1 2 3 Full support for high mass accuracy instrumentation using a high mass accuracy scoring Improved performances for the chromatograms and spectrum viewer Filters for MS level and polarity Bug fixed to handle spectra with no precursors information with negative m z and i
64. ules with high confidence HSS Ga ED SmileMS E SmileMS meets these needs and proposes a unique LC MSMS library search solution thanks to the following key benefits Intuitive Highly intuitive interface for rapid routine analysis and comprehensive results review Its intuitive interface makes it appropriate for routine applications of small molecule identifications and allows experts to evaluate the results in detail Results are delivered in aggregated lists of identified analytes supported with chromatogram and annotated spectra Reliable Powerful library search capabilities delivering highest level of confidence SmileMS is designed to identify analytes from MS spectra of fragmented molecules via a spectral library search approach It can be used both for targeted and untargeted screening methods Its robust and innovative algorithm allows for confident identification of molecules across different instrumental architectures and acquisition methods SmileMS user manual 6 v1 2 May2011 Versatile One single software for multiple MS instruments libraries and application fields The software can handle MSMS and MS3 data from a wide range of MS vendors providing a single entry point for a battery of heterogeneous instruments A large range of spectral libraries can be uploaded and queried simultaneously or separately as provided by NIST AB SCIEX Wiley VCH etc as well as privately created SmileMS has been alre

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