MassBank User's Manual
Contents
1. Empty line If you include peak information for more than one spectrum put a blank line between each one 2 Load spectral file and set the compare parameters 1 Load the spectral file Click Browse and select a spectral file Afterwards click File Read then Spectral Browser reads the spectral file and display the spectra in it Spectral Browser Hore Sveciu Qus Peak Suecus Peak aber By rer tee Spectral Browser ver 1 06 25 0 m a E tlh Lh alls id that A li 93 0 27 2 224 au W 5 p 026 2 Set the compare parameters Click Compare Parameter The Setting window opens aul aL m 69 1 04 0461 il ooa Ve TM 2 Settings e Tolerance m z error range e Cutoff Threshold Relative intensity threshold Na Hit Match Dis abi 9 Peak Pres sor show all m z show match miz change color 1 n top angle side angle Glat compare lt 2 d_09 ir I 5 l N Tolerance o3 i unit C ppm Help Cutoffthreshold 5 Help Compare Parameter Setting Window Copyright 2006 MassBank Project 29 MassBank User s Manual ul Mass Ba nk 3 Perform the compare When you specify an arbitrary spectrum as a query then you can compare input spectra in one to many manner o ppp aaa 1 Select query spectrum Comparison Window Click a radio button for selecting a query l The one to m2. 0 940870 2 6 Diethylaniline MS MS QqQ CE 10 V Moss 320 1 Methyladenosine MS MS QqQ CE 40 V 0 857132 MassBank User s Manual si MassBank lt lt Operation 3 gt gt Brief display of chemical structure Results 5 704 Hit 1 182 Displayed First Prev Next Last Total 28 Page Results End BI 82 12Z Octadecadienoate C18H3202 5 spectra H Aminomethyl phosphonate CH6NO3P 12 spectra T Methylthio acetate N 92 122 Octadec R Mandelate 15204734 7 A S 2 Aminobutyrate Multiple Display Spectrum Search Total 28 Page T Results End EL XN C18H3202 6 spectra C3H6025 2 Aminobuty Copyright 2006 MassBank Project 25 MassBank User s Manual all Mass Bank gt gt mass difference When click the mass difference button on the Multiple Display panel of Compound and Peak Search Results spectra display the peaks with the value of m z difference from that of the molecular related ion Multiple Display mass calculator user manual Formula C10H15N KO002678 2 6 Diethylaniline MS MS QqQ CE 20 V M H Exact Mass 149 12045 lt gt gt gt show all m z mass difference KO002802 2 6 Dimethylaniline MS MS QqQ CE 20 V M H Formula C8H11N Exact Mass 121 08915 Click mass difference _ lt lt lt gt gt gt show all
3. 4 Displayed ET Search First Prev 1 Next Last Total 7 Page LO A tme Format metre v Results End dihydroxyphenylacetic acid 4 Hydroxyphenylacetic acid Indole 3 acetic acid First Prev 1 Next Last Total 7 Page Copyright 2006 MassBank Project C8H804 spectrum C8H803 1 spectrum C10H9NO2 168 04226 152 04734 a Results Top 11 MassBank User s Manual l Mass Bank 3 2 Find Compounds by Chemical Structure The Substructure Search enables you to find compounds including the specified chemical structure gt gt Enter Search Parameters Query1 Query2 upo ve oo OO C JME Molecular Editor Novartis Pharma AG Peak Search Option m z Tolerance of m z 2 Peak Search option 1 Number of rr electrons e Query structure target structure default M GOs ica jw DB molfile Keio e Query structure lt target structure M m e No comparison Ov swmasuso TAE an s T NUN A 3 K0000001 mo 3 KO000012 mo 3 KO000023 mo 5jKO000034 ets Ji SamplePlugin 3 K0000002 mo 3 KO000013 mo 3 KO000024 mo 3KO000035 de Visual Studio 2008 3 KO000003 mo 3KO000014 mo 3 KO000025 mo 3 KO000036 2 Peak Search option ovs di services M ees sore Maie ne MN n Apache2 KO000005 m E KO000016 mo a KO0000027 E KO000038 os Specify m z values to perform peak search Oo gh ste
4. RT 3785 Exp 3 icavHegnovP l J 8 Scar640 oates rvonoto _ Cincbufotalin LO ESI IT TOF WS KM CH3COOH HI pcena Jl I 4 Lejeme Remtems mnnera EE Uc IEEEER puer l TL T1 L 10 Scan549 m Phosphatidylethanolamine alkenyl 180 245 LC MS MS Orbitrap m z 80459 M H RT 37 85 Exp 3 cewwOPI 11 Scan544 o4204 TYO00102 Cinobufctalin LC ESIHT TOF MS CH3COOH H c26 3407 J I J 42 Scans48 00876 UT002244 Phosphatidylserine 181 220 200 2011 LC MS MS Orbitran m z 64461 M H RT 51 49 Exp 2 ic47HponooP J f J J 05831 PRO50557 Acetylsalicylic acid ESI QTOF IMS MS MERGED M H ceuo4 f qJ scares oto noewe _ Cinobufotaa LO ESHIT TOF MS lwcicoo H O eem 1 o3157 Tvoo0102 Cinobufctslin LC ESI IT TOF MS V CH3COOH H cusor l l j 9 ee oe es L E a Lees jprws neenus sese Lo eser ene IH emon e l _ e280 o omohtislO Esr TOF MS M CHnCOOH E 9 Scan555 i 01108 UTOQ2898 Phosphatidylethanobmine alkenyl 180 245 LC MS MS Orbitranl m z 80459 V H RT 3785 Exp 3 oggNO P l 20 Scan556 Acetylsalicylic acid ESI Q TOF MS MS MERGED M H C8H804 Scan958 C Hit Record gt Scan559 0 1074 UT002896 Phosphatidylethanolamine alkenyl
5. j side angle Change angle side perspective ee flat Change angle all spectrums in flat view Copyright 2006 MassBank Project l7 MassBank User s Manual ul MassBa nk 2 2 Spectrum Search on Quick Search Page The Quick Search feature allows you to search for similar spectrums just using simple input gt gt Enter Search Parameters Qu ick Search 3 manual in Japanese Quick Peak Substructure Peak Advanced Browser Batch Browse Index You can narrow your results by selecting the Instrument type or lonization Mode Die ot hes 1n TA HEIL ER III II yr E MS GC EI TOF MS Enter peak data ESI CE ESI TOF MS ESHT MS n ESHT MS MS r ESI QqIT MS MS ESI QqQ MS MS ESI QqTOF MS MS LC ESHT TOF MS LC ESI Q MS Ao ESraATAC MOMS lonization Mode Positive Negative Both m z and relative intensities 0 Example1 Example2 Cutoff threshold of relative intensities v 1 2 Number of Results 20 v Search 1 Cutoff threshold of relative intensities Single space Relative intensity threshold Ignore peaks with intensity lower than specified 273 096 A 22 value EN M d 2 Number of Results dud Intensity Number of retrieved spectrums to be displayed Absolute or relative value can be used gt gt Display Search Results Quick Search Results 91 096 Display query spectrum Previous Query Results 20
6. merged type ion mode and compound name categories same format as other search results Record Index Contributor Instrument Type MS Type Merged Type lon Mode Compound Name 1 Contributor Number of data listed by contributors Chubu Univ 2 628 IMM CAMS amp PUMC China 67 Kyoto Univ 185 NAIST 817 Osaka Univ 502 Tottori Univ 16 Univ Toyama 253 gt CE ESLTOF 20 ELEBEB 12 ESLQqQ MS MS 52 FAB EB 5 F B 1 LC ESLIT 515 LC ESLQ 2 721 LC ESLQTOF 2 742 Normal 28 560 Positive 22 721 1 273 1 117 565 1 389 1 491 lt M E 0 gt mM I Z Ilio 2 Instrument Type Number of data listed by the types of chromatography and mass spectrometer 3 MS Type Fac Eng Univ Tokyo 12 379 Kazusa 273 Leibniz IPB 528 Nihon Univ 75 PFOS research group 277 UOEH 35 Waters 2 994 CLB 796 ESHT MS MS 149 ESHQqTOF MS MS 510 FAB EBEB 173 GC ELFTOF 1 016 LC ESHTFT 3 006 LC ESLQIT 378 MALDI TOF 17 MS 16 898 MS2 11 505 Merged 839 Negative 6 678 C 1 478 777 Number of data listed by the types of mass spectrometry 4 Merged Type Number of merged ESI MS2 data and that of the other data 5 lonization Mode Number of data analyzed by positive and negative modes 6 Compound Name Number of data listed by the first letters of compound names Copyright 2006 MassBank Pro
7. Settings Make sure that your Web browser is configured as follows 1 JavaScript execution enabled 2 Popups enabled See the page below for instructions on how to check this URL to allow http www massbank jp http www microsoft com japan windowsxp using web sp2 popupblocker mspx 3 Install Java runtime environment The Java Runtime Environment JRE Version 5 or higher must be installed You can use the page below to check your installation status and download Java http www java com en download Copyright 2006 MassBank Project 3 ul MassBank MassBank User s Manual 2 Searching for Similar Spectra 2 1 Spectrum Search Applet opectrum Search enables you to perform GUI based spectrum searches in a Web browser Spectra in the MassBank similar to one provided by the user as a query are retrieved and displayed in a list It is also possible to graphically compare the query spectrum with the retrieved spectrum 1 Prepare the query file When performing a spectrum search with the applet you must prepare a query file in one of the following formats A sample can be downloaded from http www massbank jp sample sample zip Query File Contents Name Write an arbitrary name such as the name of the compound Optional 70 24 Peak information Write the m z and Name Sample Compound 2 intensity separated by 73 1 15008 spaces You can write all 78 54 4456 the peak information on a 70 45 21583
8. Type CE ESI TOF MS ESI IT MS n ESI IT MS MS ESI QTOF MS MS ESI QqIT MS MS ESI QqQ MS MS ESI QqTOF MS MS LC ESI F T MS LC EST IT MS M S LC ESI IT TOF MS LC ESI Q MS LC ESI QTOF MS MS LC ESI QqQ MS MS LC ESI TOF MS Ion Mode Negative Name Scan530 gt Name of a query spectrum Hit Top 20 List Accession KNAO0756 KNA00487 KNA00752 KNA00542 KNA00475 KNA00628 KNAO0728 KNA00812 KNAO0820 KNAO00554 KNA00538 KNA00527 KNA00648 KNA00736 KNA00808 KNA00491 KNA00483 KNAO0696 KNAO0546 KNAO0530 LIst of search results at most 20 high scored spectra Title Formula Mass Score L Aspartate LC ESI FT MS NEG L Aspartate LC ESI FT MS NEG L Serine LC ESI FT MS NEG cis Aconitate LC ESI FT MS NEG L Serine LC ESI FT MS NEG L Glutamine LC ESI FT MS NEG L Homoserine LC ESI FT MS NEG CAH9NO3 Citrate LC ESI FT MS NEG C6H807 3 Phospho D glycerate LC ESI FT MS NEG L Homoserine LC ESI FT MS NEG CAH9NO3 sn Glycerol 3 phosphate LC ESI FT MS NEG S Malate LC ESI FT MS NEG C4H605 L Threonine LC ESI FT MS NEG CA4H9NO3 L Asparagine LC ESI FT MS NEG C4H8N203 cis Aconitate LC ESI FT MS NEG C6H606 L Glutamine LC ESI FT MS NEG C5H10N203 L Asparagine LC ESI FT MS NEG C4H8N203 4 Hydroxy L proline LC ESI FT MS NEGCBH9NO3 D Gluconic acid LC ESI FT MS NEG C6H1207 2 Oxoglutarate LC ESI FT MS NEG C5H605 C4H7NO4 CAH7NO4 C3H7NO3 C6H606 C3H7NO3 CSH10N203 Copyright 2006 MassBank Project Hit 133 0375
9. m z but by the assigned molecular formulae MassBank recommends the query data that is enough high in the resolution to assign the molecular formula to peaks All possible peak differences in the target are also calculated by the molecular formulae Peak differences between the target and the query are compared by the molecular formulae Additionally the present tool evaluates the matching peaks observed in the range of m z 50 99 gt gt Input the query data and set the parameters Metabolite Identification Home Spectrum Quick Peak Substructure Identification Browser Batch Browse Index MassBank ID Go by Peak Substructure Relationships e by Annotated Neutral Losses 1 Query File Ae File Read sample file 4 sample archive Search similar spectra on a neutral loss to neutral loss basis Retrieves spectra similar to user s spectrum in terms of molecular formulae This search is helpful to predict the chemical structure of unknown metabolites 1 Select by Annotated Neutral Losses 2 6 the same in the Section 5 1 Metabolite prediction based on peak chemical substructure relationships Copyright 2006 MassBank Project I 19 MassBank User s Manual l Mass Bank gt gt Search Results Matched neutral losses B A list of the peak differences that were HIN 17 027 CH2N2 42 022 CAHB amp 54 047 CHSN3 59 048 C3H70 53 05 C4H3N 71 074 annotate
10. the box it is added and merged into the query With each selection the merged ESI MS data generated is shown in the right window 5 Set parameters see the table below All the parameters should be set correctly Input Precursor m z 61 Click Search button to start Paremeters settings Merge Select ON when two or more ESI MS2 data are merged into the query Check box is appeared at each data Select the data by checking their boxes Leave OFF default to predict the metabolite from a single data Cutoff This selects the product ions for the prediction Only the peaks larger than the cutoff value are considered in the prediction Cutoff value is indicated by the red dotted line on the merged spectra in the write window Precursor ion is always included in the prediction independent of the cutoff value Tolerance This defines the mass accuracy of the product ions in the query data Within the tolerance substructure peak relationships give possible substructures to each product ion Precursor m z in the red box Check whether the precursor m z is correct When the nvz value is not correct correct it manually Precursor m z in the white box This defines the mass accuracy of the precursor m z lon Mode Select either Positive or Negative Precision This is the precision of an empirical relationship between a peak and a chemical substructure that is used for prediction Fal
11. you chose selected in step 2 then you can hold down Ctrl Shift to select multiple There are two display modes in Package View rows If you chose related in step 2 Different Display Modes in Package View selected then only one row can be selected Multiple spectrums can be selected from the list of search results The selected spectrums and the query spectrum are shown in a tiled view related Only one spectrum can be selected from the list of search results The selected spectrum a spectrum with different collision energy than the selected spectrum detected automatically and the query spectrum are displayed in tiled view Peak Color in Spectrum Comparison Window In the spectrum comparison windows in Compare View and Package View matching peaks can be distinguished by color Matching m z on query peak Perfect Match Match within Error Margin Retrieved Spectrum Red Pik Query Spectrum Copyright 2006 MassBank Project i 5 MassBank User s Manual ul Mass Bank lt lt Handy Feature 1 Spectrum Zoom gt gt 1 Select location to zoom Drag from the location of the start of the zoom 2 Set zoom position Drop to set the location on the spectrum to zoom 3 End zoom Double click on the spectrum Note You can also zoom on spectrums from the Package View Seep oom scope n E i ww Example from Compare View Handy Feature 2 Peak Manipulation gt gt Example from Compa
12. 1 133 03751 105 04259 174 01644 105 04259 146 06914 119 05824 192 027 C3H707P 119 05824 C3H9O6P 134 02152 119 05824 132 05349 174 01644 146 06914 132 05349 131 05824 196 0583 146 02152 0 3545 0 3104 0 3041 0 2955 0 2942 0 2911 0 2904 0 2885 185 99294 0 2823 172 01367 0 2746 0 2716 0 2713 0 2673 0 2663 0 2650 0 2646 0 2616 0 2587 NJ NJ NJ NJ NJ NJ NA N 0 2844 N 0 2756 NINNNNNNNN lo MassBank User s Manual ill Mass Bank 2 Summary of Results HTMLformat Summary Of Batch Service Results Request Date 2010 10 15 14 07 51 JST Instrument Type CE ESI TOF MS ESI IT MS n ESI IT MS MS ESI TOF MS MS ESI OqIT MS MS ESI O qQ IMS MS5 ESI Qq TOF MS MS LC ESI FT MS LC ESI IT IMS MS LC ESI IT TOF MS LC ESI O MS LC ESI QTOF MS MS LC ESI QqQ MS MS LC ESI TOF MS lon Mode Negtve List of the best hit for each query eee Q N MassBank ID Record Title F Colored Pathway Maps uery Nam ssban eco ormula AE ues pua 1 Ewsao oases KRAUS Aerertrte LC ESIFT MS MEG ber Duns Barth e Ts Cg estes eeseweneoecem VR 5 E aiii 3 Scu boso ewegS Seweic tsrrwe wa A e esonwGS Lie sss favors ptam ce serre es temor ame Freeones Ls Beers pswe owes esse MS MS 090 E10 RE i o exe ef No Hit Record gag a ed 7 Scan539 LESE Phosphatidylethanolamine alkenyl 180 245 LC MS MS Orbitrap m z 80459 M H
13. 11 multiple lines writing one 85 3 964800 peak per line 86 11 150 90 0 804911 Name Sample Compound 3 178 876379147 15 186 884786287 8 229 504276894 9 Empty line If you include peak information for more than one spectrum put a blank line between each one 2 Load the query and configure the search parameters Spectrum Search After selecting your abl la GUSH fe Click File H Ne Sa Hone Spect Quick sels Subst s Compare View Package View Cutoff Threshold v CE ESI TOF MS Y ESLIT MSn v ESLIT MS MS v ESI OTOF MS MS v ESI OgIT MS MS Y ESI OqQ MS MS e Positive Negative Both Cancel Search Parameter Setting Window Copyright 2006 MassBank Project ame Sample Compound 1 UNE PY Single space Sample ame Arbitrary name When entering a name always begin the line with Name Single space 8 54 4456 Em mvz Intensity Absolute or relative value can be used 1 Load the query file Click Browse and select the query file you have prepared Click File Read to load the file After the file finishes loading a list of queries appears 2 Set the search parameters Click Search Parameter Setting The Setting window opens Settings e Precursor m z Precursor ion specified by m z e Tolerance m z error range e Cutoff Threshold Relative intensity
14. 180 245 LC MS MS Orbitrap m z 80459 M H RT 37 85 Exp 3 ca7Heano7P J e utem Tis 1286 PB004142 Kaempferot MS MS QaQ CE35 eV M HI c15H1008 coseos e Tmapot 1002 7 24 Scan562 No Hit Record wd m 180 201 181 200 LC MS 3 Orbitrap m z 81657 72915 M H w Serl RT 4392 B 2 casHeenooP J Ll f J as sansa oes nonae pnctwira LG ESHHT TOF wS TwecooCoOH HE owe 1 Vl1 1 E 2 Senso Ye ea oe a5 Seans67 poer vroes _ turechenodeonycholte MS MS T m z 4083 WEHE cmo mes C pests 29 Scan568 V0 4084 TYOO0 0 Cinobufotalin LC ESIHT TOF MS M CH3COOH H Click a link then the pathway map is displayed In the pathway map the best hit compounds of all queries are highlighed L td wm f CF Qu l1 DRUG METABOLISM OTHER ENZYMES Azathioprine amp 6 Mercaptop urine Trinotecan Innoteean SN 38 32 131 In global map map 01100 Other than glovbal map the best hit compounds are Fluorouracil The best hit compounds are highlighted in black Capctte ete highlighted in red CYP2A6 3 orca open ond p nm i O gt excretion sper pe pen o 321 eo 3315 o Beg excretion meu a 5 Fluorouridine 5 Fluorouridine monoph
15. 8 MassBank User s Manual ul Mass Bank 5 2 Metabolite prediction by spectrum search in terms of neutral loss Chemical compounds are often synthesized from a common chemical compound by slight chemical modifications Such derivatives share the chemical structure of the common chemical compound Their mass spectra are also similar although their similarity cannot be detected by conventional spectral similarity search Peaks observed in the mass spectrum of one derivative are shifted by u from the corresponding peaks of the other one where is the mass difference between their chemical structures Such a similarity is searchable by comparing not the m z of the corresponding peaks but the mass difference between the corresponding peak pairs because is unknown Thus this tool searches the ESI MS data in MassBank that are similar to the query one by comparing the m z difference between the corresponding peak pairs Here neutral loss is defined as the m z difference between peak pairs Search results suggest the users the common chemical compound among the target and query chemical compounds However this comparison has such a general difficulty that many possible peak pairs should be compared within the mass accuracy of m z To escape the difficulty the targets in the present method are limited to the high resolution MassBank ESI MS2 data with chemical annotation on peaks All possible peak differences in each target data have been calculated not by
16. G MS MS QqQ CE 30 V M H Ti MS MS QI qe 0 V IH MS MS QqQ GE 50 V M H MassBank Record KO002806 Home Specinm Quick Peak Substuctu Pas Adiances rower Balch Browse idex Record No cc 2 4 Dimethytaniline MS MS QqQ CE 10 V M H Mass Spectrum 222 Eros Copyright C 2006 2008 Institute for Advanced Biosciences Keio University i ACCESSION K0002806 i RECORD TITLE 2 4 Dimethylaniline MS MS QqQ CE 10 V M H i DATE 2007 07 07 AUTHORS Kakazu Y Horai M Institute for Advanced Biosciences Keio Univ COPYRIGHT Copyright C 2006 2008 Institute for Advanced Biosciences Keio University Copyright 2006 MassBank Project Close All Tree Multiple Display v Results End 5 spectra KO002806 KO002807 KO002808 KO002809 KO002810 5 spectra KO002677 KO002679 KO002680 KO002681 121 08915 5 spectra KO002801 KO0002803 KO002804 KO002805 MassBank record of an individual spectral data is displayed 23 MassBank User s Manual lt lt Operation 2 gt gt ll MassBank Interaction with Multiple Display and Spectrum Search Results 25 Hit 1 25 Displayed First Prev 1 Next Last Total 7 Page lt Close All Tree K Multiple Display J C pectrum Search D DD nme o rosee 2 O El 2 4 Dimethylaniline C8H11N 5 spectra m MS MS QqQ CE 10 V M H MS MS QqQ CE 20 V M H MS M
17. Hit Show Spectra Spectrum Search Up to top 20 scores displayed a i e 3 3 5 7T Pentahydroxyflavan LC TOF MS C15H1406 3 3 5 T Pentahydroxyflavan LC TOF MS C15H1406 Desalkylflurazepam LC Q MS POS 15 V 45 V C15H10CIFN20 Copyright 2006 MassBank v Is ill MassBank MassBank User s Manual 2 3 Conduct Batch Spectrum Searches Batch Service conducts a batch spectrum search and emails you the results Use this in such cases as when you would like to search for a large number of spectra Batch Service ieubmit Mail Address ttek keio ac jp Copyright since 2006 2009 JST BIRD MassBank 1 Load the query file Prepare a query file with the same format as the one described in 2 1 1 Spectrum Search Applet Click Browse and select the query file you have prepared 2 Enter email address Enter the email address to which you would like the search results sent Click Submit to perform the batch query A message appears indicating that the query has been accepted Batch Service 2009 09 25 18 41 51 Your batch search is accepted The results will be sent to ynihei ttck keio ac jp later Search results are sent to the specified address by e mail The following files are attached to the e mail 1 Search Results and 2 Summary of Results 1 Search Results Text Format MassBank Batch Service Results Request Date 2010 10 15 14 07 51 JST Instrument
18. It is highlighted in blue and the m z and intensity values appear b Select peak Click on a desired peak It is rendered in blue to indicate that it is selected Up to 6 peaks can be selected Peak Rendering Color Highlighted Blue Selected Light blue c Search for peaks If you right click while one or more peaks are selected a menu appears and Peak Search can be selected The peak search begins immediately after selection d Cancel peak selection Select Select Reset from a menu popped up by a right button click in graphic area Peak Search Results Window Highlight amp select peak in Spectral Browser In Spectral Browser when you highlight or select a peak in a spectrum peaks in other spectra are also highlighted or selected if whose m z are completely equal to the m z of the highlighted selected peak lt lt Handy Feature 3 Spectrum Manipulation gt gt Spectral Browser ver 1 06 73 0 4 ab tk em amid game US000006 US000005 US000004 US000003 US000002 US000001 Compoeund 02 Compound 01 Copyright 2006 MassBank Project Copyright C since 2006 2009 JST BIRD MassBank Spectrum Manipulation Buttons c lt a 2 2 Move display location only when zoomed on spectrum show all m z Display mvz values of all peaks show match m z Display m z values o
19. S QqQ CE 30 V M H m MS MS QqQ CE 40 V M H MS MS QqQ CE 50 V M H O El 2 6 Diethylaniline m C10H15N 5 spectra MS MS QqQ CE 10 V M H MS MS aaa CE 30 V Izd M MS MS QqQ CE 30 V M H Clicking Show Spectra Multiple Display mass calculator 4 user manual Home Spectrum Quick Paak Substructure Peak Ackancad Browser Batch Browse index MassBank D Formula CT0H15N J Exact Mass 149 12045 2 r al E 1 gt gt gt show all mz mass difference Formula CBH11N 002002 2 5 Dimetindandine MS MS QuO CE 20 V M H 5 Exact Mass 121 08915 22 2 NH Ke CH i6 9 lt lt lt gt J gt snow an mz mass amorence The selected spectra are displayed in tiled view Clicking Spectrum Search KO002806 KO002807 KO002808 KO002809 KO002810 149 12045 KO002677 KO002679 KO002680 KO002681 121 08915 KO002801 KO0002803 Spectrum Search s8 sample file sample archive Wil 4 Compare View M Package View Package View display mode selected related lt lt lt gt P show a mi Search Parameter Setting The Spectrum Search page opens and the selected spectra are added to the query Click a button displaying a record title to show the MassBank record MassBank Record KO002678 Home Spectrum Qu
20. TOF MS data are shown Kei ad RIKEN Copyright 2006 MassBank Project l 28 MassBank User s Manual l Mass Bank 7 4 Comparison Tool of User Spectra Spectral Browser is a comparison tool of spectra which reads a file which consists of a set of user spectra and displays them in perspective drawing The upper limit of user spectra is 20 It also compare input spectra each other 1 Prepare the spectral file The format of an input of Spectral Browswer so called a spectral file is as follows You can download a sample from http www massbank jp sample sample zip The format of this spectral file is same as the format of a query file of Soectrum Search then a spectral file is commonly used in Spectrum Search Spectral Browser Spectral File RU Single space ame Sample Compound 1 24 ame Sample Arbitrary name Peak Information When entering a name always begin Write the m z and the line with Name intensity separated by spaces You can write all the peak information on a multiple lines writing one peak per line Name Write an arbitrary name such as the name of the compound Optional Name Sample Compound 2 73 1 15008 79 45 2158311 85 3 964800 86 11 150 90 0 804911 Single space 8 54 4456 T m z Name Sample Compound 3 178 876379147 15 186 884786287 8 229 504276894 9 Intensity Absolute or relative value can be used
21. Y NC SA COMMENT KEIO ID M057 tY oJu seg CHSNAME S Mandelate CHSNAME S Mandelic acid CHSNAME S 2 Hydroxy 2 phenylacetic acid CHSNAME 5 2 Hydroxy 2 phenylacetate CHSCOMPOUND CLASS Non Natural Product CHSFORMULA C8H803 CHSEXACT MASS 152 04734 CHSSMILES OC 0 C H O c c1 cccci CHSIUPAC InChI 15 C8H803 c9 7 8 10 11 6 4 2 1 3 5 6 h1 5 7 9H H410 CHSLINK CAS 90 64 2 611 72 3 CHSLINK CHEBI 32800 CHSLINK CHEMPDB SMN CHSLINK KEGG C01984 CHSLINK PUBCHEM SID 5081 CH NAME name can include multiple names including variants CH FORMULA Molecular formula CH EXACT MASS Exact mass to five decimal places CH SMILES SMILES code CH IUPAC InChl code ACSINSTRUMENT instrument name AC INSTRUMENT TYPE instrument type AC MASS SPECTROMETRY MS TYPE ms type AC MASS_ SPECTROMETRY ION MODE ion mode ACSINSTRUMENT API3000 Applied Biosystems ACSINSTRUMENT TYPE LC ESI QQ ACSMASS SPECTROMETRY MS TYPE MS2 ACSMASS SPECTROMETRY ION MODE NEGATIVE ACSMASS SPECTROMETRY COLLISION ENERGY 30 V MSSFOCUSED ION PRECURSOR M Z 151 MSSFOCUSED ION PRECURSOR TYPE M H SUO IPUOD jeon Apeuy Oju PUNOdWOD PKSNUM PEAK 8 PKSPEAK m z int rel int 59 200 707921 5 999 77 200 232673 5 328 92 000 613862 0 866 105 100 99010 0 140 107 200 198020 0 279 108 300 193069 5 272 133 000 34653 5 49 136 200 460396 5 650 PK NUM PEAK number of peaks ejeq y
22. ak pairs Abd RR ae Copyright C 2006 2008 Institute for Advanced Biosciences Keio University Copyright C 2006 2008 ACCESSION KOX006 RECORD TITLE S Aussiwo yame vraw aS Tee i Fa d s i ACCESSION KOX00710 RECORD TITLE Dihydrosphingosine MS MS Qq Copyright 2006 MassBank Project 14 MassBank User s Manual Assist in the Input of Molecular Formulas l MassBank When m z values instead of molecular formulas are entered in the Formula boxes a list of candidate molecular formulas whose exact masses are close to the entered m z values is shown in the pull down menu Following example shows a case when a value 141 was entered in a Formula box on the Search of Peaks and Search by Molecular Formula mode Search of Peaks 5 Peak Differences Search by m z Value Molecular Formula Formula Formula Formula 141 AND AND 141 00103 O i 141 01072 141 04527 141 0664 141 07043 141 11402 141 12794 141 13917 d are only Keio and Riken data sBank Search of Peaks Peak Differences Search by m z Value Molecular Formula ormule Formula Formula Come e no AND OOR The targets of Peak Search Advanced are only Keio and Riken data Copyright amp since 2006 2010 JST BIRD MassBank Copyright 2006 MassBank Project 15 MassBank User s Manual ull Mass Bank 5 Prediction of Metabolites from ESI MS Data 5 1 M
23. any comparison is suddenly cr iy Li cab di ad 0L executed and its results are reflected d ie automatically 27 2 Display query and others T had i04 re Toric Name Hit Match Disable Precursor ID A ol pousld 09 0 O 67 US000009 C m L t ompound_08 6 US000008 O pari S O n S ompound_07 J15 US000007 mpound_06 21 US000006 mpound 05 a d US000005 ompound 04 US000004 ompound 03 US000003 ompound 02 US000002 ompound 01 US000001 SOOS N wean 4 co Copyright C since 2006 2009 JST BIRD MassBank Peak Color in Spectrum Comparison Window In the spectrum comparison windows in Compare View and Package View matching peaks can be distinguished by color Query Spectrum Red Red Retrieved Spectrum O Red Pink O Handy Feature 1 Spectrum Zoom gt gt 1 Select location to zoom Drag from the location of the start of the zoom 2 Set zoom position Drop to set the location on the spectrum to zoom E Les amos changgffoior EET top angie side angi 3 End zoom Double click in comparison window then return to the initial size without zooming use Pel ELE Tel po Copprgtt C mace 2005 2008 JST DRD Marla Copyright 2006 MassBank Project 30 MassBank User s Ma
24. assBank User s Manual 4 2 Peak Search with Molecular Formulas Peak Search Advanced enables you to find peaks by specifying an ion or neutral loss by molecular formulas instead of a numerical m z values gt gt Enter Search Parameters Searching via ion Searching via neutral loss Search of Peaks Peak Differences Search of Peaks Peak Differences Search by m z Value Molecular Formula Search by m z Value 2 Molecular Formula Formula Formule Lora OFFRE Formula Formula E Gomer aus Enter molecular formula Enter molecular formula AND OR AND S SEQUENCE gt The targets of Peak Search Advanced are only Keio and Riken data The targets of Peak Search Advanced are only Keio and Riken data Er Toa gt gt Display Search Results Query Query CAH7NO2 CH4S C5H6N5 AND C3H6N Edit Resubmit Query Edit Resubmit Query Results 1 Hit 1 1 Displayed Results 1 Hit 1 1 Displayed First Prev 7 Next Last Total 7 Page First Prev 7 Next Last Total 7 Page E C41 S Adenosylmethionine gt gt Spectrum View Searching by lon MassBank Record KOX00710 Dihydrosphingosine MSAN QqTOF MERGED M H C18H40NO2 Mass Spectrum Molecular formulas with nin matching peaks appear pm pb lt lt lt snow all miz lt lt lt gt gt gt show an miz Molecular formulas with matching pe
25. cted Display multiple spectra in a tiled view Mutiple Display in popup menu by right button click when multiple spectra are selected Copyright 2006 MassBank Project 22 MassBank User s Manual 7 Others 7 1 Search Results sl MassBank When you conduct a search via Quick Search Substructure Search Peak Search Peak Search Advanced or Record Index the search results are displayed in a common format lt lt Operation 1 gt gt List of Search Results Results 25 Hit 1 25 Displayed Compound list 1 Next Last Total 7 Page First Prev HE 3 4 Dimethylaniline Fi B2 Wethylaniline 1 Bl 2 64 aniline q Open All Tree Multiple Display Spectrum Search NY v Results End Formula Structure ExactMass ID C8H11N ue NL08915 5 spectra CY N l C10H15N 5 spectra C8H11N 121 08915 S 5 spectra Spectrum list Results 25 Hit 1 25 Displayed First Prev 1 Next Last Total 1 Page o El 2 4 Dimethylaniline MS MS QqQ CE 10 V M H MS MS QqQ CE 20 V M H MS MS QqQ CE 30 V M H MS MS QqQ CE 40 V M H MS MS QqQ CE 50 V M H 2 6 Diethylaniline OOOWoOoO MS MS QqQ CE 10 V M H MS MS QqQ CE 30 V M H MS MS QqQ CE 40 V M H MS MS QqQ CE 50 V M H El 2 6 Dimethylaniline OOOOWO L MS MS QqQ CE 10 V M H e
26. d with the molecular formula in the query data No 2 KOX00653 Agmatine MS MS agroF MERGED M H CENCE Hits 5 No 3 KOX00672 Bufarmin MSvMS QaTOF MERGED M H LETTEIEEE Hits 4 H3N 17 027 H3N 17 027 H3N 17 027 CH2N2 42 022 CH2N2 42 022 CH2N2 42 022 CAHB 54 047 CAHB 54 047 CH5N3 58 048 CH5N3 58 048 CH5N3 58 D48 CAHSN 7 1 074 CAHSN 1 074 Ce GR ABB ABRBBRBMABBRBBBBBS Aidit tt t t t t CHENG 0 05617 Exact Mass IEMA men Formula C6H15N5 CARNE Ds Exact Mass 157 13275 77777 ee Formula Ch5H14N4 TEN ME Exact Mass REIA Fate No 4 KOX00641 No 5 KOX00781 No 6 KOX00737 Metformin MS MS GgqTOF MERGED M H b Guanidinapropianate MSMS GgTOF MER Hits Hits 3 H3N 17 027 H3N 17 027 du o Aaa a CHSN3 59 048 CH5N3 58 048 Wii jee es Hits 3 H3NI 1 7 0271 CAHB B4 D47 CAHAN 1 074 CHBN3 EU 0581 7 i CHBN3 ED D5817 Formula C4H11N5 Formula CA4H9N302 CON RN H Exact Mass 129 10145 Exact Mass 131 06948 lon CAH1ON 72 08132 Formula CoH14N20 Exact Mass MassBank data similar to the query one are shown max 30 data Neutral Loss Here Neutral Loss is defined as the difference of the corresponding peak pairs in terms of molecular formulae The target data are listed b
27. eed PK PEAK array of m z measured intensity and relative intensity for each peak yh 9 For details of MassBank Record see Record Editor Manual Copyright 2006 MassBank Project l 27 MassBank User s Manual ul Mass Bank 7 3 Basic Mass Calculation Tool Mass Calculator on the upper right corner is a basic mass calculation tool that you can use everywhere in MassBank t calculates m z i e exact mass of the input formula or displays a list of chemical formulae corresponding to m z 3 mass calculator user manual 1 Click mass calculator MassCalculator appears in a separate window Calculation of m z from chemical formula Listing of chemical formulae corresponding to m z Mass Calculator Mass Calculator Formula to m z m z to formula Formula to m z Formula miz mz Formula C18H3202 C3H6028 C8H803 280 24023 5 CloHi6O 152 12012 D IC1OH18N 152 14392 IC11H40 152 02621 Basedondata y Ag 152 06260 152 04734 from Keio and IC2H3NO5S 152 97319 Riken CZH4NOSP 152 98271 CSH6NO4S 152 00175 IC3HEOSP 152 99528 IC3HSN203P 152 03508 C4H8045 152 01433 C5SCIN3O 152 97299 4 106 00885 9599985 1 Select Formula to m z 2 Select m z to formula 3 Input Formula 3 Input m z When a formula is entered m z is calculated and When a m z value is entered the chemical displayed formulae that were observed in the MassBank annotated ESI Q
28. ered onmi Elrond Hiean Become at same time NS ple eon Bias Boneia use 3Ko000010 mo 3Ko000021 mo 3 KO000032 mo 3 koo00043 li 3Ko0000011 mo 53K0000022 mo Ko000033 mo 3 koo00044 cov 23449 mJ FI 274 WEM KODCOQ0Q mol 35002741 gt gt Display Search Results Query1 Edit Resubmit Query Results 48 Hit 1 42 Displayed Open All Tree Multiple Display Spectrum Search First Prev 1 2 Next Last Total 2Page v Results End O E R Phenylephrine C9H13NO2 w 167 09463 1 spectrum On Ow Bl 1 10 Phenanthroline C12H8N2 180 06875 2 spectra J Copyright 2006 MassBank Project 12 MassBank User s Manual ul Mass Bank 4 Peak Search 4 1 Peak Search by m z values Peak Search enables you to find peaks by specifying the m z or m z difference as numerical values gt gt Enter Search Parameters 1 Search of Peaks or Peak Differences 1 Search of Peaks Peak Differences Peaks search of the m z value 2 Searchby e m z Value Molecular Formula Peak Differences search of the m z differences 2 Search by m z Value or Molecular Formula 3 Select m z Value for Peak Search by m z values Formula AND v 79 05477 3 mz ai Specify the peak m z value You can specify up to 6 and AND connect them via AND or OR conditions AD e 4 Rel Intensity AND I Ignore peaks with
29. etabolite prediction by using peak chemical substructure relationships Currently this tool is adapted to predict primary metabolites and their derivatives from the query ESI MS data MassBank has analyzed and accumulated the relationships between peaks product ions and chemical substructures by chemically annotating ESI MS data of primary metabolites The present tool elucidates possible chemical substructures of the unknown metabolite from the query ESI MS data by using the relationships that linked the observed product ions to chemical substructures Additionally possible molecular formulae of the unknown metabolite are predicted from the precursor ion KNApSAcK database lt hittp kanaya naist jp knapsack jsp top html gt provides a list of metabolites that satisfy the predicted molecular formula with the possible chemical substructures Finally the prediction tool outputs the list as the candidates of the unknown metabolite A reliable prediction is expected when 1 the query ESI MS data should be analyzed on high resolution mass analyzers 2 the precursor ion observed is a type of M H 3 more than ten product ions with the relative intensity higher than 5 96 are observed 4 a query data that was prepared by merging two or more ESI MS data analyzed on the same unknown metabolite at different CID conditions gives a good result The present tool automatically merges them into a single query data gt gt Input the query data and
30. f matching peaks change color Change color of entire spectrum s l Change angle manual manipulation top angle Change angle top perspective side angle Change angle side perspective flat Chanae anale all spectrums in flat view 31 MassBank User s Manual ull Mass Bank lt lt Handy Feature 4 Sort Spectra gt gt 1 Sort Spectra n um Click one of header items in comparison list P Vds meses ie Order Query Name Hit J i Match Disable Peak Precusor and ecl La f ID then the list is sorted by the item Consecutive clicks of an item change the order of sorting cyclically in ascending descending and without sorting 2 Cancel sorting Select Sorting Cancel in a menu popped up dig EE by right button click on comparison list 0233580 226 3237 Il f n top angle side angle fiat compare 5 Hit Match Disable Peak Precursor L 67 O Compound 07 2 Compound 06 Compound 05 Compound 04 Compound 03 J Compound 02 Je Compound 01 t m US000001 Copyright C since 2006 2009 JST BIRD MassBank lt lt Handy Feature 5 Spectrum Hiding gt gt Spectral Browser ver 1 06 a Hide show spec ru m For each item in comparison list tick its checkbox Disable then the corresponding spectrum is hided Untick the checkbox the
31. ick Peak Subsructue Peak Achanced Browser Batch Bova indes Recon 2 6 Diethylanitine MS MS QqQ CE 20 V M H Mass Spectrum I lt lt show all miz CopynghtiC 2006 2008 Insstute for Advanced Biosciences Keio University ACCESSION KO002678 RECORD TITLE 2 6 Diethylaniline MS MS QqQ CE 20 V DATE 2007 07 07 M AUTHORS Kakazu Y Horai H Institute for Advanced Biosciences Keio Univ COPYRIGHT Copyright C 2006 2008 Institute for Advanced Biosciences Keio University CHSNAME DEA CHSNAME 2 Diethylaniline CHSFORMULA CLOHLEN CHSEXACI MASS 145 12045 CH SMILES CCce c1 c N e CC ecl CHEIUPAC 1 CLOHLSN cl 3 8 6 5 7 5 4 2 10 8 11 h5 7H 3 4 1182 1 283 CHSLINK CAS 75 66 8 CHSLINK KEGG C11001 CHSLINK KEIO D035 CHELINK NIKKAJI JE5 263 CHSLINK PUBCHEM SID 13 84 Copyright 2006 MassBank Project You can search with the selected spectrum as the query Spectrum Search ail Package View Compare View KO002802 2 5 EITI MS MS QqQ CE 20 V M H aJ adiu il A 1 related lt lt lt gt P gt show att miz 2 6 Diethytanitine MSMS Qq0 CE 20 V IM HI Package View display mode selected Search Parameter Setting Score Hitl 2 6 Diethylaniline MS MS QqQ CE 20 V M 0 899998 21 KO00 a 14 KOXO Kono je Koon 2 6 Diethylaniline MS MS QqTOF MERGE
32. intensity lower than specified value Specify a relative intensity from 1 to 999 AND e 4 5 5 Tolerance Specify the m z error range Search Display Search Results Results 313 Hit 1 46 Displayed Close All Tree 5 First Prev 723456789 Next Last Total 9Page Formula Structure ExactMass 1 Adamantanamine C10H17N 151 13610 L MS MS QqQ CE 40 V cum C10H17N 151 13610 L MS MS QgQ CE S0 V oO C10H17N 151 13610 m L S lt Clic C10H17N 151 13610 E 1 Methyladenine C6H7N5 149 07015 L MS MS QqQ CE 40 V M H C6H7N5 149 07015 L MS MS QqQ CE 50 V M H C6H7N5 149 07015 1 Adamantanamine MS MS QqQ CE 40 V M H Mass Spectrum Mass Spectrum ACLOO a TU Matching peaks are colored atching peak pairs are colored lt lt lt gt gt gt show all mz a Copyright C 2006 2008 Institute for Advanced Biosciences Keio University lt gt gt gt show an miz ACCESSION K0002186 Copyright C 2006 2008 Institute for Advanced Biosciences Keio University RECORD TITLE 1 Adamantanamine MS MS QaQ CE 40 V M H DATE 2007 07 07 ACCESSION KO002304 AUTHORS Kakazu Y Horai H Institute for Advanced Bioscience RECORD TITLE 5 Aminoimidazole 4 carboxamide 1 ribofurano COPYRIGHT Copyright C 2006 2008 Institute for Advanced Bios DATE 2007 07 07 Copyright 2006 MassBank Project 13 sill MassBank M
33. ject Click a link in this page then the whole data in the category is displayed in the mass calculator XS user manual Fukuyama Univ 340 Keio Univ 5 629 Metabolon 149 Osaka MCHRI 20 RIKEN 1 722 Univ Connecticut 510 ELB 11 636 ESI QalT MS MS 15 FAB B 26 FD B 41 LC APPLQQ 277 LC ESHTTOF 253 LC ESI QQ 5 038 395 1 371 262 21 MassBank User s Manual all MassBa nk 6 2 Hierarchical Browse In Browse Page all data are hierarchically displayed for each data provider You can go up and down the hierarchy tree and find a specific data you want B rowse Page mass calculator user manual in Japanese I3 e IAB Keio Univ RIKEN PSC Nihon Waters K K Kyoto University Fac Med Univ Tokyo Kazusa DNA Res Inst Nihon University University of Toyama Tottori University Leibniz IPB Germany Fac Eng Univ Tokyo Fukuyama University Metabolon Inc Univ Occu Env Health Grad Sch Info Sci NAIST Osaka Medical Center for MCH University of Connecticut 1 Select Provider Click a radio button then display the hierarchy of the selected provider is displayed in right hand side 2 Browse Tree open the lower layer close the lower layer 3 Display Spectrum View detailed MassBank Record Double click of W or Show Record in popup menu by right button cllick when a spectrum is sele
34. m mass difference Multiple Display mass calculator user Formula C10H15N Exact Mass 149 12045 45 0 t 27 8 105 300 949 887 dai ci1sepi S ans tage Ludo rl s lt gt gt gt show all m z mass difference Formula C8H11N Exact Mass 121 08915 Difference of m z from that m z of molecular of the molecular related ion related peak 3293 35 1 1 qme 573 99 P29 ans 269 lt lt gt show all m z mass difference Copyright 2006 MassBank Project 26 MassBank User s Manual all Mass Bank 7 2 MassBank Record Detailed Display The MassBank record is the fundamental unit of data in the MassBank database Each mass spectrum has one MassBank record In addition to peak data each record includes the compound information CH test conditions AC etc To see Record Editor Manual for more details MassBank Record KO001419 S Mandelic acid LC ESI QQ MS2 CE 30 V M H Mass Spectrum Chemical Structure lt lt lt gt show all m z ACCESSION record ID HECORD TITLE title compound name method etc DATE Date last updated Create date AUTHORS Record creators LICENSE Creative Commons or Copyright ACCESSION KO001419 RECORD TITLE 5 Mandelic acid LC ESI QQ M52 CE 30 V M H DATE 2011 05 10 Created 2007 07 07 AUTHORS Kakazu Y Horai H Institute for Advanced Biosciences Ki LICENSE CC B
35. n it appears again b Hide show all spectra Select All Disable in a menu popped up by right button click on comparison list then all spectra are hided Select All Enable in the same menu then all spectra appear again Order Query J Compound 04 2 Compound 03 2 Compound 02 ej Compound 01 44 DOO I All Disable 4 AllEnable jUSO00008 US000002 A uso00001 Copyright C since 2006 2009 JST BIRD MassBank Comparison window and comparison list Comparison window and Comparison list are operated simultaneously For example spectra are sorted in comparison list the results is suddenly reflected to comparison window and spectra in comparison window are also sorted in same order Copyright 2006 MassBank Project l 32 Contact Please contact the MassBank Group if you have any problems or questions massbank iab keio ac jp 81 235 29 0800 ull MassBank http www massbank jp
36. nine MS MS QqQ CE 40 V M H Aa sow aimo UTTMA TIC NOT 1221 9 TTHPIEAIS C Vm TM b Show multiple spectra When you right click with two or more spectra selected the Show Spectra command appears on the menu Select ms at ma Clvomne MAI Gq CE40 V rte euer mon iD ato bem P bas ani L this to display multiple spectra in tiled view 1 iim MSAIS QgQ CE 40 V Mehe 0 456 Jtketyiguanine MEMS QgO CE 30V M 0451885 mone MSMS Og C 30 v M H 10 450030 DO di eune MSMS QQ CE 30 Weie 42 E 5 x Multiple Display T tiare cto Quick Ple uentus Prae dec Cer Estat Eres tees isola D show ait mz show match m z change color 1 1 top angie sme angie tat Mate D Deanie Contributor j 8 0002155 KeioUnw 03 x 2534 Keio Lini Example from Package View Handy Feature 4 Spectrum Manipulation gt gt Se Spectrum Manipulation Buttons in Compare View oe Sy Se Se Move display location only when zoomed on spectrum show all m z Display m z values of all peaks show hit m z Display m z values of matching peaks Spectrum Manipulation Buttons in Package View de Sy Sy SS Move display location only when zoomed on spectrum show all m z Display m z values of all peaks show match m z Display m z values of matching peaks change color Change color of entire spectrum fr Change angle manual manipulation top angle Change angle top perspective
37. nual lt lt Handy Feature 2 Peak Manipulation gt gt Spectral Browser ver 1 06 ul MassBank Pesci jj40565 42 Ai i 107 0732 196 9 lt lt lt gt gt gt snow all m z show match miz change lor l i n top angle side angle fiat compare parameter Selected m z 110 0 b ay Order Query _ Name Hit Match Disable Peak Precursor ID 9 Compound 09 LJ 6 US000009 8 Compound 08 6 L 12 US000008 7 J Compound 07 15 Lj j108 US000007 6 Compound 06 214 LJ 31 US000006 5 Compound 05 9 L 27 US000005 4 2 Compound 04 9 16 US000004 3 J Compound 03 B3 LJ 7 US000003 2 O Compound 02 55 LJ 180 US000002 1 Compound 01 64 109 US000001 Peak Search Results Home Spectsur Quick Peg petatur Peg Adenced Search Parameters ovr 1100 Rem amp Toluit 0 ketrument Type AN lor zaton Mode Both Results 2 904 Hit Fe Pov 1223450198 9 10 st Total 97 Page Formula Structure Name E 17 ME THYL TESTOSTERONE C20H3002 1 specum El ALPHA CYPERONE C120 1 specum E ALPHA MUUROLENE C15 04 1 spectrum E CAMPHOR C1000 1 un F CIHCHONINE C19622N20 yun Copyright C sinte 2006 2009 JST BIRD MassBank 302 22458 218 16707 204 10700 152 12012 294 17321 a Highlight peak Place the cursor over a peak
38. of neutral loss 19 5 BIOWSIHO AU Datla 5 2 32 20 8 02 924 0 6 05 609 2 0 8500000 00 EE E aiai araia 21 oT Gaeo INIG Rm 21 oe PETOG EONS E arsar E EEEE EEEE EEEE 22 Fe OG S a E E ee ene eee ee 23 ONES eau 23 7 2 MassBank Record Detailed Display cccccccccccsseececceeceecseeeceeeeeeeeesseeeeessaaeeeesaeseeessaeeees 27 73 Basic Mass Calculation I00L coii uaa etu roo vus atc ooa a aaa tun a rer awa 28 7 4 Comparison Tool of User Spectra ssssssessssssssssssssseeeeeeeennnnn nennen nennen nnns 29 Copyright 2006 MassBank Project i 2 MassBank User s Manual ill MassBank 1 Introduction This manual mainly describes the operation of the MassBank database services 1 1 Overview of the Database Services MassBank provides the following database services Database Service 9pectrum Quick Search Search Peak Substructure Metabolite Search Search Identification Spectral Browser gt Batch Service Browse Page gt Record Index Compare spectra in perspective drawing See p 28 Hierarchical browse of all spectra See p 21 Categorical index by instrument type et al See p 20 1 2 System Requirements Below are the system requirements for using the MassBank database services 1 Web Browser We recommend using Internet Explorer 6 or higher or Firefox 2 or higher as your browser 2 Web Browser
39. osphate Hydmzine 24 24 O 27 121 O 5 Fluorodeoxyuridine monophosphate 5 Fluorodeox yuridine 00923 2 16 10 c Kanehisa Laboratories Copyright 2006 MassBank Project i 10 MassBank User s Manual ul MassBank 3 Compound Search 3 1 Find Compounds on Quick Search Page The Quick Search feature allows you to search for compounds by compound name molecular formula etc gt gt Enter Search Parameters Quick Search manual in Japanese You can narrow your results by selecting the Instrument type and lonization Mode EI MS GC EI TOF MS OCE ESI TOF MS OESIHT MS n OESIHT MS MS CJESI QqIT MS MS JESI QqQ MS MS L ESI QqTOF MS MS L LC ESHT TOF MS L LC ESI Q MS Mie EGI OTOC MOIM lonization Mode Positive Negative Both 1 Compound Name Enter the compound name Names with substring matches on the string you entered are retrieved 2 Exact Mass Tolerance Enter the exact mass and error tolerance 3 Formula Enter the molecular formula of the compound Enter the formula starting with C followed by H and then the other letters in alphabetical order Add wildcards to find partial matches Example C5H N5 gt gt Display Search Results Quick Search Results mass calculator user manual Go Search Parameters Compound Name acetate Instrument Type GC EI TOF MS lonization Mode Positive Edit Resubmit Query Results 4 Hit 1
40. re View Example from Package View a Highlight peak Place the cursor over a peak It is highlighted in blue and the m z and intensity values appear b Select peak Click on a peak It is rendered in blue to indicate that it is selected Up to 6 peaks can be selected c Search for peaks If you right click while one or more peaks are selected a menu appears and Peak Search can be selected The peak search begins immediately after selection d Cancel peak selection When you right click on the spectrum a menu appears Chose Select Reset 5 2 6 Deethytaniline E 2 Hydroxyhexanoate m4 a rien Peak Rendering Color Peak Search Results Window Highlighted Blue Selected Light blue Highlighting and Selecting Peaks in Package View When multiple spectrums are displayed in Package View you can highlight or select the peaks in any spectrum When you do so if there is a peak in another spectrum with a perfectly matching m z then that peak is also highlighted or selected Copyright 2006 MassBank Project i 6 dll MassBank MassBank User s Manual Handy Feature 3 Show Record gt gt a Show record When you right click with one spectrum selected the Show Record command appears on the menu Select this to view Example from Compare View details about the spectrum MassBank Record KO002877 Home Spectum Quack Pact Substructure Peal Advanced Dover E Gatch Eos index Recodo Ethio
41. s between peaks and chemical substructures B Candidates of the unknown metabolite are shown The KNApSAcK database outputs the candidates that satisfy the following conditions they have one or more of the substructures shown in A and the molecular formula is the same to that predicted from the mass of the precursor ion A substructure in the gray box in A is not applicable in the candidates in B Formula Precision amp Recall TP precision 0 66 S i csHN X o6 o 68 27 C5H4 recall 0 68 p Formula Precision amp Recall TP C5HAN 0 66 0 68 27 in the above example Formula Chemical formula of a peak Precision Ratio of the number of ESI MS data pyrimidine substructure amp C5H4N to that of ESI MS data C5H4N where among the ESI MS data C5H4N in which the peak C5H4N was observed ESI MS data pyrimidine substructure amp C5HAN are those analyzed on chemical compounds with the pyrimidine substructure In the above example the ratio is 0 66 Recall Ratio of the number of ESI MS data pyrimidine substructure amp C5H4N to that of ESI MS data pyrimidine substructure where the ESI MS data pyrimidine substructure were analyzed on chemical compounds with the pyrimidine substructure In the above example the ratio is 0 68 TP Total number of the ESI MS data pyrimidine substructure amp C5H4N In the above example it is 27 Copyright 2006 MassBank Project i 1
42. se positive decreases with the precision See the next page for details Copyright 2006 MassBank Project i 17 MassBank User s Manual ull Mass Bank gt gt Search Results Matched Formulae 4 mz 79 0355 20 0508 96 0458 123 0560 Formula C5HAN C5H6N C5H6NO onn ru m z Product ions used for prediction Formula Possible molecular formulae assigned to the ions No ID numbers of the substructures predicted by the relationships between peaks and chemical substructures No ion pos 0013 ion pos 0013 ion pos 0013 ion pos 0013 Hit Relationships 2 Substructure Substructure N 6 By placing the cursor on an ID number the corresponding substructure is shown as A Formula Precision amp Recall TP csHeNo 0 55 0 55 11 Formula Precision amp Recall TP C5H4N o 66 0 68 27 ceHzN20 joez o1 4 csHeN C5H4N 0 71 0 38 15 _ AT ass lariana a anla acl Results 3 Hit Isonicotineamide Nicotinamide Picolinamide Formula C6H6N20 Formula C6H6N20 N Formula C6H6N20 Exact Mass 122 048 Exact Mass 122 04801 Exact Mass 122 048 DB Links DB Links DB Links KEGG C02421 KNApSAck C00000209 KEGG C01950 j KEGG C00153 Ni N Hit Relationship No Hit Relationship No Hit Relationship No ion pos 0013 ion pos 0013 ion pos 0013 A Possible substructures that are embedded in the structure of the unknown metabolite are predicted by using the relationship
43. set the parameters The following procedure shows a case when three ESI MS data analyzed on the same unknown metabolite at different CID conditions are uploaded merged into a single query data and predicted Metabolite Identification Home Spectrum Quick Peak Substructure Identification Browser Batch Browse Index MassBank ID Go t1 9 by Peak Substructure Relationships by Annotated Neutral Losses 2 Query File File Read sample file 4 sample archive 1 Select by Peak Substructure Relationships 2 2 Load the query file A list of the ESI MS data Select the query file uploaded is shown Click File Read To prepare the query ESI MS file see 2 1 1 Prepare the query file No Name Peak 1 samplel_CEl Qewv 2 samplel CEZQOew 3 sample1l CE30ewv 4 sample2 CET1QOewv 5 sample2 CE20eV mum ma D a dnd wn fe on fe amp i i L 3 ED 100 mz 5 spectra 3 Merge of Cutoff so Tolerance 0005 2 show all m z Precursor m z RR 0000 S lon Mode Positive precision 04 3 Set Merge On d A check box 3 is appeared at each data Copyright 2006 MassBank Project 16 MassBank User s Manual ll Mass Bank 3 sample E 4 sample2_CE10eV 4 El 5 sample _CE20eV 5 5 spectra show all m z 4 By checking the box select the data files of the metabolite to be identified As one data is selected by checking
44. sill MassBank MassBank User s Manual Version 2 4 7 February 2012 Copyright 2006 MassBank Project MassBank User s Manual ul Mass Bank CONTENTS LEN oi igero U eji o o ett 3 1 1 Overview of the Database Services sssssssssssssssssseeseeeeenenn nnne nennen nennen nnne nani rr 3 ONE i i Fev renen S LEE 3 2 Searching for Similar Spectra 1 1leee leere eL eee liess e ieen nennen nena nana nnns 4 BA Spectrum Search AO Sl E o OO TET 4 2 2 Spectrum Search on Quick Search PagQe ccccssssssssssssssssssssssssssssssssssessessesseseesssesseeeeeeees 8 2 9 QGonduct BAICM SOSCINUM Oe are IBS s uccouuutiutioci ono ap t BUUeC E E UNUM URSSUU UU UU UUE 9 3 Compound Search os eee ewes de sere UEM cU wa ana anan a ana Eee ERE s COE aaia anana 11 9 1 Find Compounds on Quick Search Pagos oou unu unum unu U Uu UU US Uu UU UNUU UND USSN NON NUN NUEUEUE 11 3 2 Find Compounds by Chemical Structure ccccccccsssscececeeeecseeeseeeceeeeeeseeeeseeeeeeeeesssaaeeeeeeeees 12 a PEAK DOANGCWN E 13 41 Pedecoedren Dy JUEZ ValUBS ssim UDIN NRI 13 4 2 Peak Search with Molecular Formwulas essen 14 5 Prediction of Metabolites from ESI MS Data sssssssscesesssseseseseseeeeeseeneteneaeaeens 16 5 1 Metabolite prediction by using peak chemical substructure relationships 16 5 2 Metabolite prediction by spectrum search in terms
45. threshold e Instrument Type Type of instrument e lonization Mode Mode of ionization l4 MassBank User s Manual ul Mass Bank 3 Perform the search Compare View Compare query and retrieved spectrums one to one Conn Ol 1 Select Compare View Query specirum Click to select It is selected by default Jia a DINNER CN 2 Select the query spectrum Click to select the spectrum to use in Query spectrum the query As soon as it is selected similar spectrums are retrieved Retrieved spectrum Spectrum comparison on ve ts er e nnum reri Retrieved sbectrum 3 Select a retrieved spectrum epee tee Click to select any spectrum in the list DUCI AT U EE 22 1 of search result List of Search result oe d it Cutoff threshold 5 show af m Ethwonine MSMS QqQ CE 40 V M H Package View Compare query and retrieved spectrums one to many 1 Select Package View gt Sp Freeh Click to select iris l 2 Select package view display mode ectrum i Click selected or related i meme dl TA a Retrieved spectrums n 3 Select the query spectrum A Click to select the spectrum to use in mo ES nactus the query As soon as it is selected similar spectrums are retrieved 10 Resun FisEof search result List o amp sp ctrum comparison 4 Select a retrieved spectrum IT E Click to select any spectrum in the list of search result If
46. y a total number Hits of the molecular formulae that were matched between the query and target ESI MS data lon The matching peaks 50 m z 99 are listed by molecular formulae They are shown in a dotted red box when the target data have the maximum number of matching peaks The target data that have no matching peak are shown in a grey box They are not shown when the hide button was clicked Results NO peaks within m z 50 99 in query is shown when no peak 50 m z 99 was observed in the query data Results NO matched ions to peaks within m z 50 99 in query is shown when no peak 50 lt m z lt 99 has no annotated molecular formulae Exact Mass Molecular mass of the target data is shown in white characters in the red box or in the grey box when it is equal to Precursor m z 1 or Precursor m z 1 in the positive or negative mode respectively Rank The target data are listed by the rank which is scored by a total number of matching peak pairs with matching peaks Minimum requirements that target data are matched or similar to the query are as follows Target data are ranked at high They have one or more matching peaks 50 m z lt 99 Their molecular mass is equal to that of the query Copyright 2006 MassBank Project l 20 MassBank User s Manual 6 Browsing All Data 6 1 Categorical Index sill MassBank In Record Index all data is categorized into contributor instrument type MS type
Download Pdf Manuals
Related Search