Manual Mass Bank

MassBank Users Manual
Version 2.3, 9 December 2010
Copyright 2006-2010 JST-BIRD MassBank
CONTENTS
1. Introduction ................................................................................................................... 3
1.1 Overview of the Database Services .......................................................................................... 3 1.2 System Requirements ............................................................................................................... 3
2. Searching for Similar Spectra ...................................................................................... 4

2.1 Spectrum Search Applet ............................................................................................................ 4 2.2 Spectrum Search on Quick Search Page .................................................................................. 8 2.3 Conduct Batch Spectrum Searches .......................................................................................... 9 2.4 Spectral Search by Annotated Neutral Loss .............................................................................11
3. Compound Search ...................................................................................................... 13

3.1 Find Compounds on Quick Search Page ................................................................................ 13 3.2 Find Compounds by Chemical Structure ................................................................................. 14
4. Peak Search................................................................................................................. 15
4.1 Peak Search by m/z values ..................................................................................................... 15 4.2 Peak Search with Molecular Formulas .................................................................................... 16
5. Browsing All Data ....................................................................................................... 18

5.1 Categorical Index ..................................................................................................................... 18 5.2 Hierarchical Browse ................................................................................................................. 19
6. Others .......................................................................................................................... 20
6.1 Search Results ........................................................................................................................ 20 6.2 MassBank Record Detailed Display ........................................................................................ 24 6.3 Basic Mass Calculation Tool .................................................................................................... 25 6.4 Comparison Tool of User Spectra ............................................................................................ 26
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.
Spectrum Search applet See p. 4 Spectrum Search on quick search page See p. 8 Find Compounds on quick search page See p. 10 Peak Search with numerical m/z See p. 15 Find Compounds by chemical structure See p. 14 Spectrum Search by annotated neutral loss See p. 11
Compare spectra in perspective drawing See p. 26
Submit batch spectrum searches See p. 9
Hierarchical browse of all spectra See p. 19
Categorical index by instrument type et.al. See p. 18
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 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/seminar/help/popup.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/
2. Searching for Similar Spectra

2.1 Spectrum Search Applet
Spectrum 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
Name
Write an arbitrary name, such as the name of the compound. (Optional)
[Query File Contents]

Single space Name: Sample Compound 1 70 24; 71 10; 72 68; 73 999; 74 107; 75 162; 76 13; 77 40; 78 3; 79 7; 80 1; 82 7; 83 5; 84 9; 85 9; 86 22; 87 8; 88 4; 89 2; 90 1; Name: Sample_Compound 2 73.1 15008; 78.54 4456; 79.45 2158311; 85.3 964800; 86.11 150; 90.0 804911; Name: Sample Compound 3 178.876379147 15; 186.884786287 8; 229.504276894 9; 360.7581988508 12;
Name :
Sample
Arbitrary name
Peak information
Write the m/z and intensity, separated by spaces and semicolons. You can write all the peak information on a single line, or use multiple lines, writing one peak per line.
When entering a name, always begin the line with "Name:"
Single space
78.54
m/z
4456 ;
Empty line
If you include peak information for more than one spectrum, put a blank line between each one.
Intensity (Absolute or relative value can be used) Enter semicolon as a delimiter
(2) Load the query and configure the search parameters

[1]
After selecting your query file, click File Read.
[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.
Query list view
[2] Set the search parameters

Click Search Parameter Setting. The Setting window opens. [2] Settings Precursor m/z Precursor ion specified by m/z Tolerance: m/z error range Cutoff Threshold: Relative intensity threshold Instrument Type: Type of instrument Ionization Mode: Mode of ionization Search Parameter Setting Window
Click Search Parameter Setting
(3) Perform the search Compare View: Compare query and retrieved spectrums one to one.
[1]
[1] Select "Compare View"

Click to select. It is selected by default.
Query spectrum
[2]
[2] Select the query spectrum Spectrum comparison

[3] Query spectrum Click to select the spectrum to use in the query. As soon as it is selected, similar spectrums are retrieved.
Retrieved spectrum
Retrieved spectrum List of search result
[3] Select a retrieved spectrum

Click to select any spectrum in the list of search result.
Package View: Compare query and retrieved spectrums one to many.

[1]
[1] Select "Package View"

Click to select.
Spectrum comparison
[3]
[2] Select package view display mode

[2] Click "selected" or "related". Retrieved spectrums
[3] Select the query spectrum

[4] Query spectrum Click to select the spectrum to use in the query. As soon as it is selected, similar spectrums are retrieved.
List of search result
List of spectrum comparison
[4] Select a retrieved spectrum

Click to select any spectrum in the list of search result. If you chose "selected" in step 2, then you can hold down Ctrl + Shift to select multiple rows. If you chose "related" in step 2, then only one row can be selected.
Different Display Modes in Package View There are two display modes in Package View. 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 Peak Query Spectrum Red Red Retrieved Spectrum Red Pink
<<Handy Feature 1: Spectrum Zoom>> [1] Select location to zoom

[3]
Overall view
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. [1] [2] Note: You can also zoom on spectrums from the Package View.
Select zoom scope Example from Compare View
<<Handy Feature 2: Peak Manipulation>> Example from Compare 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 b a
b. Select peak a
c d
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".
Peak Search Results Window
Peak Rendering Color 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.
<<Handy Feature 3: Show Record>> a. Show record

When you right click with one spectrum selected, the "Show Record" command appears on the menu. Select this to view details about the spectrum.
Example from Compare View
b. Show multiple spectra

When you right click with two or more spectra selected, the "Show Spectra" command appears on the menu. Select this to display multiple spectra in tiled view.
Example from Package View
<<Handy Feature 4: Spectrum Manipulation>> Spectrum Manipulation Buttons in Compare View

<< < > >> show all m/z show hit m/z Move display location (only when zoomed on spectrum) Display m/z values of all peaks Display m/z values of matching peaks
Spectrum Manipulation Buttons in Package View << < > >> show all m/z show match m/z change color top angle side angle flat Move display location (only when zoomed on spectrum) Display m/z values of all peaks Display m/z values of matching peaks Change color of entire spectrum Change angle (manual manipulation) Change angle (top perspective) Change angle (side perspective) Change angle (all spectrums in flat view)
2.2
Spectrum Search on Quick Search Page
The Quick Search feature allows you to search for similar spectrums just using simple input.
>> Enter Search Parameters
Select this
You can narrow your results by selecting the Instrument type or Ionization Mode.
Enter peak data
[1] [2]
[1] Cutoff threshold of relative intensities Relative intensity threshold Ignore peaks with intensity lower than specified value. [2] Number of Results Number of retrieved spectrums to be displayed
Single space
273.096
m/z
22 ;
Intensity (Absolute or relative value can be used) Enter semicolon or carriage return
>> Display Search Results
Display query spectrum
Up to top 20 scores displayed
Hit: Number of peaks in the retrieved spectrums matched to those in a query data Score: Similarity score of retrieved spectrum to a query data
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.
[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. [1] [2]
[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.
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 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-FT-MS,LC-ESI-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 ### Query 1 ### # Name: Scan530 # Hit: 37 Top 20 List Accession KNA00756 KNA00487 KNA00752 KNA00542 KNA00475 KNA00628 KNA00728 KNA00812 KNA00820 KNA00554 KNA00538 KNA00527 KNA00648 KNA00736 KNA00808 KNA00491 KNA00483 KNA00696 KNA00546 KNA00530 Title
Name of a query spectrum
LIst of search results (at most 20 high-scored spectra)

Formula Mass Score Hit L-Aspartate; LC-ESI-FT-MS; NEG C4H7NO4 L-Aspartate; LC-ESI-FT-MS; NEG C4H7NO4 L-Serine; LC-ESI-FT-MS; NEG C3H7NO3 cis-Aconitate; LC-ESI-FT-MS; NEG C6H6O6 L-Serine; LC-ESI-FT-MS; NEG C3H7NO3 L-Glutamine; LC-ESI-FT-MS; NEG C5H10N2O3 L-Homoserine; LC-ESI-FT-MS; NEG C4H9NO3 Citrate; LC-ESI-FT-MS; NEG C6H8O7 3-Phospho-D-glycerate; LC-ESI-FT-MS; NEG L-Homoserine; LC-ESI-FT-MS; NEG C4H9NO3 sn-Glycerol 3-phosphate; LC-ESI-FT-MS; NEG (S)-Malate; LC-ESI-FT-MS; NEG C4H6O5 L-Threonine; LC-ESI-FT-MS; NEG C4H9NO3 L-Asparagine; LC-ESI-FT-MS; NEG C4H8N2O3 cis-Aconitate; LC-ESI-FT-MS; NEG C6H6O6 L-Glutamine; LC-ESI-FT-MS; NEG C5H10N2O3 L-Asparagine; LC-ESI-FT-MS; NEG C4H8N2O3 4-Hydroxy-L-proline; LC-ESI-FT-MS; NEGC5H9NO3 D-Gluconic acid; LC-ESI-FT-MS; NEG C6H12O7 2-Oxoglutarate; LC-ESI-FT-MS; NEG C5H6O5 133.03751 133.03751 105.04259 174.01644 105.04259 146.06914 119.05824 192.027 C3H7O7P 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 2 2 2 2 2 2 2 2 0.2844 2 0.2756 2 2 2 2 2 2 2 2 2
2 2
(2) Summary of Results (HTMLformat
List of the best hit for each query
Click a link, then the pathway map is displayed. In the pathway map, the best hit compounds of all queries are highlighed
In global map (map:01100), the best hit compounds are highlighted in black.
Other than glovbal map, The best hit compounds are highlighted in red
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2.4
Spectral Search by Annotated Neutral Loss
In Advanced Search, an unknown compound is identified by a MSn spectrum by the similarity of formulae of neutral loss molecules. Even if there is not a spectrum of the correct answer in MassBank, you can obtain valuable information for compound identification by investigating some common characteristics among structures of high-ranking compounds because the similarity of structures among compounds is inherited to the similarity of detected neutral losses among spectra of them.
>> Input Search Parameters
1) Select a query file, and click File Read button.
For the format of query file, see 2.1(1) Prepare the query file.
List of the spectrua in the submitted query file.
The selected query supectrum is displayed graphically.
2) Select a query spectrum.
3) set search parameters, and click "Search" button.
Search Parameters Precursor m/z m/z of the precursor is set automatically. The default value is m/z of the right most peak in the selected query spectrum whose relative intensity is more than or equal to 50 %. If the default value is not adequate, please revise it manually. Ionization Mode Select Positive or Negative. Merge You can merge several spectra in to a query and use it as the query spectrum. When "On" is selected, a checkbox appears to each spectrum in the left sided list for specifying spectra to merge. Cut off Ignore every peak whose relative intensity is less than the specified value.
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>> Search Results

hide button Formulae and molecular weights of neutral losses detected in the query spectrum. [4] [1]
[2]
[3]
At most 30 hits of MassBank Records are displayed [1]Neutral LossNumber and formulae of neutral losses matched to ones detected in the query spectrum. Search results are sorted in descending order of the number of the neutral losses. [2]IonFormulae of ions matched to ones detected in the query where the integer value of m/z is between 50 and 99. A, Surrounded by a red dotted line: The result has the most detected ions of 30 hits in the page. (No.1, 2, 3 and 6 in this example. They have two ions which is the most in this page.) B, Black on gray: The number of ions is equal to zero. * Click hide button (in front of No.1), then these results become hidden. C, Message NO peaks within m/z 50-99 in query.: There are no peaks in query within the range. D, Message NO matched ions to peaks within m/z 50-99 in query.: There are peaks in query within the range but there are no matched peaks in the search result. [3]Exact Mass White on red: The value is projected by the precursor m/z. The precursor m/z is equal to the increment / decrement of the exact mass when the ionization mode is "positive" / "negative" (130+1 = 131 in this example). White on gray: There is 50 or more difference between the exact mass and the precursor m/z. [4]Ranking The search results are sorted in descending order of the number of the matched neutral losses in [1]. In the case of a tie, they are sorted in ascending order of the difference between the exact mass in [3] and the projected one by the precursor m/z. See the above [3] for the details of the prediction using the ionization mode.
Support Conditions on Equality or Similarity of Chemical Structure

Higher ranking. Especially in the case of [2] A. Not in the case of [2] B. In the case of "white on red" in [3]. It is mandatory for similarity of chemical structure.
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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.
Select this
You can narrow your results by selecting the Instrument type and Ionization Mode.
[1] [2] [3]
[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
Matching items (including synonyms) are displayed
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3.2
Find Compounds by Chemical Structure
The Substructure Search enables you to find compounds including the specified chemical structure.
Enter query structure [1] Write in editor
[1] [2]
(1)Number of electrons
Or: [2] Load Molfile
(2) Peak Search option (1) Number of electrons Query structure = target structure (default) Query structure target structure No comparison (2) Peak Search option Specify m/z values to perform peak search at same time.
You can also narrow your results by selecting the Instrument type or Ionization Mode.
(1) Click Browse
(2) Select a file
The loaded structure formula can be modified in the editor as well. >> Display Search Results
Query structure
14
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.
>> Enter Search Parameters [1] [2] [3] [1] Search of Peaks or Peak Differences - "Peaks": search of the m/z value. - "Peak Differences": search of the m/z differences. [2] Search by m/z-Value or Molecular Formula Select "m/z-Value for Peak Search by m/z values. [3] m/z Specify the peak m/z value. You can specify up to 6, and connect them via AND or OR conditions. [4] Rel. Intensity Ignore peaks with intensity lower than specified value. Specify a relative intensity from 1 to 999. [4] [5] [5] Tolerance Specify the m/z error range. Converting from molecular formula to m/z Enter a molecular formula the exact calculated mass in the m/z text box. The exact calculated mass is truncated to 5 decimal place. You can also narrow your results by selecting the Instrument type or Ionization Mode. >> Display Search Results
Click link.
>> Spectrum View

Peak Search
Peak Difference Search
m/z
Matching peaks are colored
Matching peak pairs are colored
15
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.
Searching via ion
Searching via neutral loss
Enter molecular formula
Enter molecular formula
If CH3COOH is entered, it is converted internally to C2H4O2 for the search.
If "SEQUENCE" is selected, peak pairs, whose m/z difference is matched to the molecular formula, are retrieved in the order of Neutral Loss 1, 2, and 3. (In the example above, order of CH4H7NO2, then CH4S)
Click link
Click link
>> Spectrum View
Searching by Ion
Searching by Neutral Loss
C18H40NO2 Molecular formulas with matching peaks appear
CH4S
CH4S C4H7NO2
Molecular formulas with matching peak pairs
16
Assist in the Input of Molecular Formulas 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.
Click C6H5O4
Pull-down menu shows a list of the molecular formulas, whose exact masses is starting from a values of 141. No molecular formula such as 140.9 are listed because prefix string match algorithm is applied.
17
5. Browsing All Data

5.1 Categorical Index
In Record Index, all data is categorized into contributor, instrument type, ionization mode and compound name categories. Click a link in this page, then the whole data in the category is displayed in the same format as other search results.
[1]
[2] [3]
[4]
[1] Contributor Category set of spectrum contributors.. [2] Instrument Type Category set of instrument types. [3] Ionization Mode Category set of ionization modes, i.e. positive and negative modes. [4] Compound Name Categorized by the first letters of compound names.
Each link is followed by the parenthesized number of spectra in the category.
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5.2
Hierarchical Browse
You can go up and down the
In Browse Page, all data are hierarchically displayed for each data provider. hierarchy (tree) and find a specific data you want.
After selecting a spectrum by clicking , you can select multiple spectra by clicking with Ctrl key or Shift key. After that, a right button click shows the following popup menu. [case of single selection]
Click Show Record, then the details of the MassBank Record are diplayed. [case of multiple selection]
Click Multiple Display, then multiple spectra are displayed in tiled view.
[1]
[2]
[3]
[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 ; or "Show Record" in popup menu by right button cllick when a spectrum is selected. Display multiple spectra in a tiled view: "Mutiple Display" in popup menu by right button click when multiple spectra are selected.
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6. Others
6.1 Search Results
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.
<<Operation 1>> List of Search Results

Compound list
Expand all trees
Click the "+" icon to expand an individual tree.
Click on a column heading to sort (by name, molecular formula, or exact mass).
Spectrum list
Click link
MassBank record of an individual spectral data is displayed.
20
<<Operation 2>> Interaction with "Multiple Display and Spectrum Search
[2] Click either of the buttons
[1] Select checkbox to select spectrum
Clicking "Show Spectra"
Clicking "Spectrum Search"
The selected spectra are displayed in tiled view.
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.
You can search with the selected spectrum as the query.
21
<<Operation 3>> Brief display of chemical structure
1) Move mouse pointer onto a thumbnail of chemical structure
2) The structure is enlarged. If mouse pointer leaves from the thumb nail, then it disappears
1) Click a thumbnail of chemical strucure.
2) Large strcuture is shown in another window. If another thumbnail is clicked, then a new window does not appear and the new structure is shown in the window. It does not disappear automatically, then you must close the window by yourself
22
>> 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.
Click mass difference
Difference of m/z from that of the molecular related ion
m/z of molecular related peak
23
6.2
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)
ACCESSION: record ID RECORD_TITLE: title (compound name, method, etc.) DATE: Date last updated AUTHORS: Record creators
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$IUPAC: InChI code CH$LINK: external database ID (link to external page)
MS$FOCUSED_IONInfo about characteristic peaks (e.g. precursor/base peak)
For details of MassBank Record, see "Record Editor Manual".
Compound info
Analytical conditions
AC$INSTRUMENT: instrument name AC$ANALYTICAL_CONDITION: measurement conditions Mode, collision energy, etc. Separation layer (e.g. GC/LC) conditions (storage time, column name, etc.)
Peak data
PK$NUM_PEAK: number of peaks PK$PEAK: array of m/z, measured intensity, and relative intensity for each peak PK$ANNOTATION: array of identifying info for each peak
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6.3
Basic Mass Calculation Tool
Mass Calculator is a basic mass calculation tool that you can use everywhere in MassBank. It is placed at the upper right corner of every search pages. It calculate m/z (i.e. exact mass) of input formula automatically.
[1]
[2]
When a formula is entered, then its exact mass will be automatically calculated inserted to the corresponding m/z input box automatically. The exact mass is truncated to 5 decimal point. Mass Calculator window can be closed by ESC key.
[1] Click mass calculator MassCalculator appears in a separate window. [2] Input Formula When a formula is entered, then m/z is automatically calculated.
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6.4
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 Spectrum Search, then a spectral file is commonly used in Spectrum SearchSpectral Browser. [Spectral File]
Name
Write an arbitrary name, such as the name of the compound. (Optional)
Name: Sample Compound 1 70 24; 71 10; 72 68; 73 999; 74 107; 75 162; 76 13; 77 40; 78 3; 79 7; 80 1; 82 7; 83 5; 84 9; 85 9; 86 22; 87 8; 88 4; 89 2; 90 1; Name: Sample_Compound 2 73.1 15008; 78.54 4456; 79.45 2158311; 85.3 964800; 86.11 150; 90.0 804911; Name: Sample Compound 3 178.876379147 15; 186.884786287 8; 229.504276894 9; 360.7581988508 12;
Single space
Name :
Sample
Arbitrary name
Peak Information
Write the m/z and intensity, separated by spaces and semicolons. You can write all the peak information on a single line, or use multiple lines, writing one peak per line.
When entering a name, always begin the line with "Name:"
Single space
78.54
m/z
4456 ;
Empty line
If you include peak information for more than one spectrum, put a blank line between each one.
Intensity (Absolute or relative value can be used) Enter semicolon as a delimiter
(2) Load spectral file and set the compare parameters

[1]
After selecting your spectral file, click File Read.
[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
[2] Set the compare parameters

Click Compare Parameter. The Setting window opens. Settings Tolerance: m/z error range
Click Compare Parameter.
Cutoff Threshold: Relative intensity threshold
[2]
Compare Parameter Setting Window
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(3) Perform the compare

When you specify an arbitrary spectrum as a query, then you can compare input spectra in one-to-many manner. [1] Select query spectrum Comparison Window
Click a radio button for selecting a query. The one-to-many comparison is suddenly executed and its results are reflected automatically.
Display query and others
[1]
Comparison List
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 Peak Query Spectrum Red Red Retrieved Spectrum Red Pink
<<Handy Feature 1: Spectrum Zoom>>

Overall view [3] Zoom [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 in comparison window, then return to the initial size without zooming
[1] [2]
Select zoom scope
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<< Handy Feature 2: Peak Manipulation>>

Highlight peak
Place the cursor over a peak. It is highlighted in blue, and the m/z and intensity values appear.
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
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.
Cancel peak selection

Select "Select Reset" from a menu popped up by a right button click in graphic area.
Peak Search Results Window

- Highlight & 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.
<< Handy Feature 3: Spectrum Manipulation>>

Spectrum Manipulation Buttons <<<>>> ... 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 Change angle (manual manipulation) top angle Change angle (top perspective) side angle Change angle (side perspective) flat Change angle (all spectrums in flat view)
28
<< Handy Feature 4: Sort Spectra>>

[1] Sort Spectra
Click one of header items in comparison list (i.e. "Order", "Query", "Name", "Hit", "Match", "Disable", "Peak", "Precusor", and "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 by right button click on comparison list.
[1] [2]
<< Handy Feature 5: Spectrum Hiding>>

a Hide/show specrum
For each item in comparison list, tick its checkbox "Disable", then the corresponding spectrum is hided. Untick the checkbox, then 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.
- 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.
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Contact
Please contact the MassBank Group if you have any problems or questions. [email protected] +81-235-29-0800
http://www.massbank.jp/

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Manual Mass Bank

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MassBank Users Manual

Version 2.3, 9 December 2010

Copyright 2006-2010 JST-BIRD MassBank

MassBank Users Manual

2. Searching for Similar Spectra ...................................................................................... 4

3. Compound Search ...................................................................................................... 13

5. Browsing All Data ....................................................................................................... 18

Copyright 2006-2010 JST-BIRD MassBank

MassBank Users Manual

Overview of the Database Services

Compare spectra in perspective drawing See p. 26

Submit batch spectrum searches See p. 9

Hierarchical browse of all spectra See p. 19

Categorical index by instrument type et.al. See p. 18

Copyright 2006-2010 JST-BIRD MassBank

MassBank Users Manual

2. Searching for Similar Spectra

[Query File Contents]

When entering a name, always begin the line with "Name:"

Intensity (Absolute or relative value can be used) Enter semicolon as a delimiter

(2) Load the query and configure the search parameters

[1] Load the query file

Query list view

[2] Set the search parameters

Click Search Parameter Setting

Copyright 2006-2010 JST-BIRD MassBank

MassBank Users Manual

[1] Select "Compare View"

[2] Select the query spectrum Spectrum comparison

Retrieved spectrum List of search result

[3] Select a retrieved spectrum

Package View: Compare query and retrieved spectrums one to many.

[1] Select "Package View"

[2] Select package view display mode

[3] Select the query spectrum

List of search result

List of spectrum comparison

[4] Select a retrieved spectrum

Copyright 2006-2010 JST-BIRD MassBank

MassBank Users Manual

<<Handy Feature 1: Spectrum Zoom>> [1] Select location to zoom

Drag from the location of the start of the zoom.

[2] Set zoom position

[3] End zoom

Select zoom scope Example from Compare View

c. Search for peaks

d. Cancel peak selection

Peak Search Results Window

Peak Rendering Color Highlighted: Blue Selected: Light blue

Copyright 2006-2010 JST-BIRD MassBank

MassBank Users Manual

<<Handy Feature 3: Show Record>> a. Show record

Example from Compare View

b. Show multiple spectra

Example from Package View

<<Handy Feature 4: Spectrum Manipulation>> Spectrum Manipulation Buttons in Compare View

Copyright 2006-2010 JST-BIRD MassBank

MassBank Users Manual

Spectrum Search on Quick Search Page

Enter peak data