Help Contents
Data in the MMCD database can be accessed through one or more of the five search engines located on the home page:
- Text-based search
- Structure-based search
- NMR-based search
- MASS-based search
- Miscellanea
Searches are activated by clicking on the
corresponding gold bar. Clicking on the search title will hide the search again,
returning the user to the main search menu. The "reset" command will clear all
input and return all values to the default setting.
The five search modules work together in an additive manner. Any search component that is activated is included in the current search. For example, one can search on a particular molecular formula (“Structure-based Search”) with specified chemical shift values (“NMR-based Search”) and tolerances and limit the search to metabolites believed to be associated with Arabidopsis (“Miscellanea”). After finishing a query, pushing the “reset” button will clear all previous input so that the system is ready for next searching.
The query engine can also be used for high-throughput searching by performing a batch mode search.
A drop-down menu lets users choose from the
following search options:
- Name/CAS/Kegg/CQ_ID/Exp_NMR
- Pubchem_SID
- ChemIDplus_ID
- CHEBI_ID
- PDB_Component_ID
Name/CAS/Kegg/CQ_ID/Exp_NMR
The default search option is Name/CAS/Kegg/CQ_ID/Exp_NMR. This option allows the user to search the database by any of the following:
- Common name
- IUPAC name
- CAS Registry Number
- KEGG Database Compound ID
- CQ_ID (MMCD compound ID)
- Exp_NMR ID (MMCD Identifier of experimental NMR data for a standard compound)
- And others: such as HMDB_ID, Beilstein Handbook Reference ID, EINECS ID, NSC ID, CCRIS
ID
As an example, a search for D-glucose could be entered as any of the following:
- D-glucose
- Grape sugar
- 6-(hydroxymethyl)oxane-2,3,4,5-tetrol
- 04-01-00-04302 (Beilstein Handbook Reference)
- BRN 1724615
- EINECS 200-075-1
- NSC 406891
- CCRIS 950
- 50-99-7 (CAS Registry Number)
- C00031 (KEGG)
- cq_00019 (CQ_ID)
- expnmr_00013 (EXP_NMR ID)
The Text-based Search Section is
equipped with a very flexible ambiguous search engine. When the checkbox
“Ambiguous search” is checked, the name search will consider as a hit any
synonym that includes the input string with a very flexible input format:
- More than two names can be entered together by separating them with a
semi-colon (;). The database will return entries containing
any of the search terms;
- Salt information will be discarded. e.g., gluconic acid sodium salt will be considered as gluconic acid;
- both *ic acid and *ate yield
the same result. e.g., “D-Gluconic acid” is equal to
“D-Gluconate”;
- Different separators can be used: e.g.
“D-(+)-glucose”, “D,+,glucose”, ”D_(+)_glucose”;
- The name also can be input as: “gluconic acid, D- “; “pentahydroxyhexanoic acid, 2,3,4,5,6-”; Or as: Dgluconicacid;
- Or even as (in arbitrary order): acid D-gluconic;
- The database also recognizes wildcards, identified
by the "*" character. For example, a search for "Glu*" returns glutamic acid,
glutathione disulfide, and glucose, as well as 95 other compounds;
- Finally, if no hit was found, the search engine
will suggest possibilities based on the search terms, e.g., input “gluose” will make the system return “no hit, do you mean
‘Glucose’?”
Pubchem_SID
Selection of "Pubchem_SID" enables searching by a PubChem Substance ID. For example, a PubChem SID search for "148583" would bring up the entry for glucose.
ChemIDplus_ID
The ChemIDplus ID search identifies compounds based on their ChemIDplus identification number. Using the ChemIDplus_ID search, a user could find glucose by entering "000050997."
CHEBI_ID
The text-based search menu includes an option to search by Chemical Entities of Biological Interest (ChEBI) identification number. A CHEBI_ID search for "17634" would bring up the MMCD entry for glucose.
PDB_Component_ID
Finally, the user can search the database by PDB Component ID. For example, search for "GLO" would bring up the MMCD entry for glucose.
Batch Mode
The Text-Based Search field contains a
"Batch Mode" bar. Clicking on this button switches the system to batch mode
and enables the user to input data from a file. The user needs to set
a numerical index (beginning with 1) corresponding to the query item, and the
separator. The search engine will return a list of compounds corresponding to
each of the search terms, and will include an option to download the results as
a text file. Finally, clicking on the “batch mode” title switches back to the normal
search mode.
For example, a txt file containing the following could be used to perform a text-based search for glucose, lactose, and caffeine:
glucose
lactose
caffeine
To use this file, the user would click "Text-Based Search," then "Batch Mode." From the Batch Mode window, the user should select "Browse," then locate the file on his or her computer. The index should correspond to the number of the column containing the search terms (1 in this example), and the separator should be set to whatever was used to separate the search terms (here, no need because only one search item per line).
In Structure_based
Search Section, one can search by:
- Structure
- Formula
- Molecular Weight (MW)
STRUCTURE
The structure can be entered by 4 different ways:
(1). Enter as a SMILES (Simplified Molecular Input Line Entry Specification) string, e.g., CC(=O)NC1C(CC(OC1C(C(CO)O)(C=O)O)O)O;
(2). Enter as an InChI (The IUPAC International Chemical Identifier) string by selecting the InChI option, e.g., InChI=1/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1 .
(3). The structure can also be input from a file through the "From File" option. The currently supported file formats can be found here.
(4). User can also draw the structure by a powerful structure editor borrowed from PubChem; clicking the "Draw Structure " button to activate it, after finishing sketch, copy and paste either the SMILES or InChI string from sketch panel into search panel. 
The
structure search can be exact matching, substructure matching, or similarity
matching. When “Stereochemistry Match” is checked, the stereochemistry
of the target structure must match that of the query structure in order to be
considered as a hit. Similarly, when “Ignore Charge” is checked, the
search engine will ignore the charge information during
matching.
FORMULA
Formula searches can be inclusive, exact, or
in a range. A search for "C6H6" will return compounds with six carbon and six
hydrogen atoms, plus any number of other atoms. A search for "=C6H6" will return
compounds with six carbons, six hydrogen atoms, and no other atoms. Searching
for "C6N0" will return compounds with six carbons and no nitrogen atoms.
Finally, a search for "C6 N1-3" will return compounds with six carbons and one
to three nitrogen atoms.Parentheses may be used to
group elements. For example, (CH2)3 is interpreted as C3H6. A more complicated example: =C4-9H6-12(CH2)2-3N0-2
Note: The Atom symbol must be entered as standard IUPAC format: e.g., "C" for carbon, ( not "c"); "Ca" for Calcium (not "ca", nor "CA")
MW
The MW option searches by average molecular weight. The following examples demonstrate the specificity of the results:
- 190: returns MW values between 189.5 and 190.5
- 190.1: returns MW values between 190.05 and 190.15
- "190-200" or "190 200" or "190:200" (two numbers separated by any nonnumerical symbol): returns MW values from 190 through 200, including 190 and 200
- "<=190" or "-190" : returns MW values less than 190 (including 190)
- ">=190" or "190-" : returns MW values greater than 190 (including 190)
- ">=190 and <=200": returns MW values from 190 through 200, including 190 and 200
- ">190 and <200": returns MW values between 190 and 200, excluding 190 and 200
- "190-200 or 280-320": returns MW values from 190 through 200, or from 280 through 320,including 190, 200, 280, and 320
Tips for sketching structure:
More Criteria
Click on the "more Criteria " button will activate more structure-based search condition with the priority from up to down (i.e, (((((Criterion_1 AND/OR/NOT Criterion_2) AND/OR/NOT Criterion_3) AND/OR/NOT Criterion_4) AND/OR/NOT Criterion_5) AND/OR/NOT Criterion_6). Clicking on the “Criterion_x” title will close the corresponding structure-based search condition module.
The input can be any combination of
chemical shift, carbon multiplicity, and connectivity. The search uses
average chemical shifts, which means that peaks split by J-coupling should be
entered as the unsplit value. (Looking for a 1D 1H or
13C raw data query? Visit http://www.bmrb.wisc.edu/metabolomics/query_metab.php
instead)
Data can be input as
follows:
- Chemical shifts can be input in groups. If data are entered on a single
line, commas can be used to separate different peaks of the same atom type, and
semi-colons can be used to separate different atom types.'999' indicates an unknown chemical shift. e.g,
C=63.288, 72.348; H=3.399, 3.791
C=999; H=999
- Carbon multiplicity can be incorporated into the search terms. (C=any; C0=CH4; C1=CH3; C2=CH2; C3=CH1;
C4=CH0), e.g,
C3=74.152, 72.348; C2=63.288
- Carbon-hydrogen connectivity can be added with parentheses. An [1H,13C]-HSQC peak can be input as:
(C3=74.187, H=3.524)
- To add both carbon-carbon and carbon-hydrogen connectivity, use both brackets and parentheses. Put the center carbon into the first set of brackets, and the neighboring carbons into the second set of brackets. Separate the sets with a colon, and use a pound symbol (#) to separate multiple neighboring carbons. As a fairly basic example, "[(C3=75.462, H=3.705)]:[(94.802, H=5.22)]" will search for two bonded carbons, each with one attached hydrogen.
- A more complicated example:
[(C4=35.1)]:[ (C3=23.3, H=2.6)# (C3=25.6, H=3.1)#(C2=20.5, H=2.4)#(C1=13.0, H=2.1)]
It refers to the pattern:
There are a number of additional options that can be modified by the user:
The Data Set menu allows the user to choose between Experimental and Empirical data. The Experimental Data set currently only contains approximately 300 compounds, but a more extensive search is available by selecting the Empirical Data option. When searching the Experimental Data set, users can also choose to specify the sample condition under which the data were collected.
If the "Include Labile H" box is checked, exchange labile hydrogen atoms, such as those bonded to nitrogen or oxygen, are included in the search. If the box is unchecked, these peaks are ignored.
The "Threshold (%)" box allows the user to set the threshold in the search selection. The threshold percentage is a comparison between the number of peaks in the intersection of the query and the target to the number of peaks the target has in total. The ratio of these two values is always between 0 and 100%, and the user can select the minimum percentage of the compounds that will show up in the search results.
The chemical shift tolerance, or how far
results can vary from the search value, can be adjusted for hydrogen and carbon
in the H_tol and C_tol
boxes, respectively. The database cannot currently be searched by nitrogen or
phosphate peaks, we will activate this function after the theoretical chemical
shift calculations have been finished.
Batch Mode
The "Batch Mode" component allows for automatic and high throughput analysis of 1D-1H, 1D-13C, 2D-[1H,13C]-HSQC/HMQC/HMBC data. For the best results, the NMR sample should be prepared under the same conditions as the standard samples used to build the database. For example, for a sample prepared in D2O, the pD should be adjusted to 7.4. HSQC spectra should be collected with high resolutions in both dimensions (e.g., 4K x 1K). Data should be in Bruker,Varian, or NMRPipe peaklist format , with chemical shift references to DSS or TMS (see below examples). The search uses chemical shift, line shape, peak intensity/width, and J-coupling patterns to search the experimental NMR data of standard compounds in the MMCD. The output is a downloadable table of compound identifications and relative concentrations.
1D data: peak list can be flat text, Bruker peak list, Varian peak list, see below examples:
(1). flat text: format: shift(ppm) intensity(arbitrary unit); note: intensity is optional, no relative concentration output if not provided. We suggest user use 500uM DSS as both chemical shift reference and concentration reference. below examples are all acceptable:
with index(must be integer), chemical shift, and intensity (note 500uM DSS was used as both chemical shift and concentration 
reference):
1 3.1299 8.64
2 3.1106 12.50
3 3.0910 9.41
4 2.1185 1.24
5 2.0986 3.14
6 2.0795 4.67
7 2.0600 2.93
8 2.0408 1.13
9 0.0000 0.20
without index:
3.1299 8.64
3.1106 12.50
3.0910 9.41
2.1185 1.24
2.0986 3.14
2.0795 4.67
2.0600 2.93
2.0408 1.13
0.0000 0.20
without intensity and DSS concentration reference:
3.1298
3.1104
3.0908
2.1186
2.0988
2.0794
2.0598
2.0405
(2).Bruker peak list; users can use the raw peak list output of Bruker XWIN-NMR software:
DU=C:/Bruker/XWIN-NMR, USER=cui, NAME=expnmr_00001, EXPNO=1, PROCNO=1
F1=3.295ppm, F2=-0.405ppm, MI=0.12cm, MAXI=36.00cm, PC=3.000
# ADDRESS FREQUENCY INTENSITY
[Hz] [PPM]
1 20924.4 1252.336 3.1298 10.54
2 20977.3 1244.571 3.1104 12.50
3 21030.9 1236.708 3.0908 11.46
4 23682.3 847.696 2.1186 1.33
5 23736.3 839.773 2.0988 2.92
6 23789.0 832.046 2.0794 4.95
7 23842.6 824.175 2.0598 2.66
8 23895.3 816.456 2.0405 1.17
9 29460.0 0.007 0.0000 0.20
(3) Varian peak list:
index freq(ppm) intensity
1 4.06946 99.3118
2 3.79149 28.1407
3 3.78844 33.7988
4 3.77826 55.0473
5 3.76807 52.5571
6 3.76095 24.9154
7 3.75789 27.7089
2D data: peak list can be flat text, or NMRPipe peak table, see below examples:
(1). flat text; format: shift1 shift2 intensity (intensity is optional, shift1 and shift2 is the proton or carbon chemical shift, the program will automatically determine which one is carbon or proton chemical shift.)
142.610 8.527 2.234671e+08
155.508 8.210 2.113134e+08
89.362 6.125 2.463572e+08
76.947 4.808 1.692275e+08
72.941 4.630 1.699664e+08
86.700 4.407 2.331415e+08
67.766 4.295 7.329752e+07
67.778 4.236 8.865544e+07
67.772 4.209 4.514265e+07
(2). NMRPipe peak table:
REMARK ROI 2D Peak Detection System, File: ./test.ft2
REMARK Detection Levels: -1.99209e+17 and 1.99209e+07
REMARK Detection: X(+/-1) Y(+/-1)
REMARK Interpolation: X(+/-1) Y(+/-1)
REMARK Noise: 1.20996e+06, Chi2-Threshold: 1.000000e-04, Local Adjustment: None
REMARK Position Tolerances: X(2.0) Y(2.0)
REMARK Sinc Detect ON, Height Adjustments: X(1.800) Y(1.200)
REMARK Sinc Detect Linewidths: X(5.0Hz) Y(15.0Hz)
REMARK Total Peaks: 9, Good Peaks: 9, Questionable Peaks: 0
REMARK Clusters: 8, Max Cluster Size: 2
REMARK ROI Spectral Axis Limits:
DATA X_AXIS 13C 1 893 158.910ppm 65.013ppm
DATA Y_AXIS 1H 1 813 8.800ppm 4.036ppm
VARS INDEX X_AXIS Y_AXIS DX DY X_PPM Y_PPM X_HZ Y_HZ XW YW XW_HZ YW_HZ X1 X3 Y1 Y3 HEIGHT DHEIGHT VOL PCHI2 TYPE ASS CLUSTID MEMCNT
FORMAT %5d %9.3f %9.3f %6.3f %6.3f %8.3f %8.3f %9.3f %9.3f %7.3f %7.3f %8.3f %8.3f %4d %4d %4d %4d %+e %+e %+e %.5f %d %s %4d %4d
1 155.845 47.587 0.007 0.024 142.610 8.527 14349.982 3411.911 2.191 3.297 23.210 7.739 155 157 46 50 2.234671e+08 9.945491e+05 1.362484e+09 0.00000 1 None 1 1
2 33.315 101.692 0.010 0.024 155.508 8.210 15647.853 3284.899 2.323 3.392 24.606 7.962 32 35 100 104 2.113134e+08 9.987751e+05 1.431732e+09 0.00000 1 None 2 1
3 661.693 457.043 0.008 0.045 89.362 6.125 8991.906 2450.711 2.330 5.998 24.681 14.081 660 663 454 460 2.463572e+08 9.850588e+05 2.655729e+09 0.00000 1 None 3 1
4 779.625 681.453 0.017 0.058 76.947 4.808 7742.730 1923.906 2.545 4.163 26.953 9.774 778 781 678 684 1.692275e+08 1.008489e+06 1.927181e+09 0.00000 1 None 4 1
5 817.683 711.877 0.012 0.045 72.941 4.630 7339.610 1852.485 2.346 4.904 24.853 11.513 816 819 709 716 1.699664e+08 9.531154e+05 1.854321e+09 0.00000 1 None 5 1
6 686.980 749.819 0.006 0.024 86.700 4.407 8724.051 1763.416 2.327 4.200 24.652 9.859 685 689 747 753 2.331415e+08 9.084896e+05 2.411753e+09 0.00000 1 None 6 1
7 866.847 769.008 0.018 0.341 67.766 4.295 6818.852 1718.371 2.167 9.530 22.951 22.371 866 868 763 772 7.329752e+07 9.218510e+05 1.118694e+09 0.00000 1 None 7 1
8 866.734 779.058 0.021 0.069 67.778 4.236 6820.048 1694.779 2.328 4.571 24.662 10.729 866 868 776 782 8.865544e+07 9.518984e+05 8.768116e+08 0.00000 1 None 8 2
9 866.785 783.617 0.038 0.247 67.772 4.209 6819.507 1684.076 2.306 4.874 24.421 11.441 866 867 781 785 4.514265e+07 9.522889e+05 3.837641e+08 0.00000 1 None 8 2
(Note: The default search is for average mass. This is appropriate for users who want to match a average formula weight to the database. Users who are interested in average mass searches should also try the M.W. search option located in structure-based search module which has several options that make it far more powerful.)
The MASS-Based Search module allows users to
search by mass spectroscopy data. Mass spec data are entered into the "Input
Mass" box. The user can adjust the tolerance for mass comparison in
the "Tol(ppm)" box. Four isotopomer composition are available:
C12N14, C13N14, C12N15, and C13N15.
The "Batch Mode" option allows users to input data from a file. The file can be:
For LC-MS / DI-MS:
(1) simple format1:
In this format, each line contains only the mass number (header line can be omitted). For example:
mass (header line)
290.175
410.0992
(2) simple format2:
In this format, each line contains retention_time, m/z value, intensity;(header line can be omitted). For example:
RT mass intensity (header line)
23.794 290.175 25.53
25.896 410.0992 21.17
Or (3). The full format, the file was formatted as in the following examples, using a tab (\t) as a separator (header line can be omitted):
|
Query_ID
|
RT
|
mass
|
abundance
|
N (out of
5)
|
|
1
|
23.794
|
290.175
|
25.53
|
3
|
|
2
|
25.896
|
410.0992
|
21.17
|
3
|
|
3
|
43.473
|
190.1358
|
24.9
|
3
|
|
4
|
56.359
|
186.0798
|
113.52
|
2
|
|
5
|
31.15
|
478.2656
|
3.41
|
3
|
|
6
|
34.102
|
154.0539
|
28.46
|
3
|
|
7
|
31.865
|
260.0798
|
100.79
|
2
|
|
8
|
10.992
|
252.1119
|
27.98
|
3
|
|
9
|
48.712
|
690.3477
|
21.11
|
3
|
|
10
|
25.385
|
380.0882
|
23.66
|
3
|
For MS/MS:
(1) flat text format:
In this format, each line contains only the m/z number and intensity (header line can be omitted). For example:
m/z RI(%)(header line)
43.039 11.732
43.163 21.947
43.288 12.490
43.662 20.877
43.786 15.942
44.035 31.576
44.160 11.076
44.284 13.181
44.409 34.026
44.658 13.873
44.782 17.807
60.227 15.838
60.476 15.184
(2). JCAMP-DX format; for example:
##TITLE= L-Alanine
##JCAMP-DX= 5 $$home made
##DATA TYPE= MASS SPECTRUM
##DATA CLASS= PEAK TABLE
##ORIGIN= UWI, Mona, JAMAICA
##OWNER= Dr Robert Lancashire
##$URL= http://wwwchem.uwimona.edu.jm:1104/spectra
##SPECTROMETER/DATA SYSTEM= Finnigan
##INSTRUMENTAL PARAMETERS= LOW RESOLUTION
##.SPECTROMETER TYPE= TRAP
##.INLET= GC
##.IONIZATION MODE= EI+
##XUNITS= m/z
##YUNITS= relative abundance
##XFACTOR= 1
##YFACTOR= 1
##FIRSTX= 0
##LASTX= 89
##NPOINTS= 17
##FIRSTY= 0
##PEAK TABLE= (XY..XY)
0,0 38,3 39,9 40,24 41,38 42,106 43,39 44,1000 45,47 46,17 55,8 56,3
70,7 71,11 73,2 74,20 89,2
##END=
The Miscellanea Search can be used to narrow
down the results from another search. Users can filter their results by order
status (MMCD collection of metabolites), category, input species, or inclusion/exclusion of specific
criteria.
Order Status
This is relevant to the collection of standard compounds in the MMCD collection. If "DONE!" is selected, only compounds that have been received will be searched. Similarly, "Ordering!" will search compounds for which an order has been placed, but which have not yet been received, and "Not Ordered" will search compounds that have not been ordered.
Category
When "Whole Database" is selected, the search will include the entire MMCD database.
Selecting "Arabidopsis" limits the search to the Arabidopsis database. This database includes the mustard family, including the species Arabidopsis thaliana and Brassica napus (ath/eath/ebna). The "Dicotyledons" option will search the following species: ath/eath/ebna/ecsi/egar/egra/egma/elco/emtr/eptp/epba/ehan/elsa/eles/estu/evvi. For more details, visit the KEGG website at http://www.genome.ad.jp/kegg/catalog/org_list.html.
When "All Plants" is selected, all plant species will be searched. When "All Species" is selected, the search will include all species in the database.
Users are also able to enter a specific species in the "Input Species" box. Multiple species can be included, e.g., ath,hsa.
Filter
The "Filter" option allows users to specify data types to be included or excluded in their search. Selecting "NMR Data" will limit the search to those compounds for which experimental NMR data are available. The "KEGG ID," "PubChem SID," and "ChemIDplus ID" options will limit the search to compounds with a KEGG, PubChem, or ChemIDplus ID, respectively. "CAS" will only return compounds with a CAS registry number. The "Organism" option will limit the search to compounds with organism information. The "PDB Component" option will limit the search to compounds with PDB Component ID.
Normal output results include the formula, molecular weight, CAS, synonyms, and structure for each compound returned. Links are also included to the relevant pages on KEGG, PubChem, ChemIDplus, CHEBI, Exp NMR, HMDB, and NMRShiftDB. The primary entry ID (CQ ID) is listed at the top of each entry.
In batch mode, the results include a table of the compounds matching the input file. The complete results for a specific compound can be accessed by clicking on the compound's primary ID, located in the CQ_ID column.
Clicking on the primary ID or the structure figure of a compound will open the record detail page.
Return to the MMCD Search Page