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Showing metabocard for Methyl pyruvate (HMDB0254610)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 13:59:20 UTC
Update Date2021-09-26 23:08:43 UTC
HMDB IDHMDB0254610
Secondary Accession NumbersNone
Metabolite Identification
Common NameMethyl pyruvate
Descriptionmethyl pyruvate belongs to the class of organic compounds known as alpha-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the adjacent carbon. Based on a literature review a significant number of articles have been published on methyl pyruvate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Methyl pyruvate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Methyl pyruvate is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0254610 (Methyl pyruvate)


  Mrv1533004261503042D          

  7  6  0  0  0  0            999 V2000
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0254610 (Methyl pyruvate)

HMDB0254610
     RDKit          3D
Methyl pyruvate
 13 12  0  0  0  0  0  0  0  0999 V2000
    2.5997    0.0368    0.2670 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3215    0.3178    0.7994 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1435   -0.0301    0.1657 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2217   -0.6253   -0.9376 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1708    0.2798    0.7518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4302   -0.0948    0.0693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2274    0.8758    1.8564 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2186    0.9586    0.1573 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5390   -0.5192   -0.6975 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1083   -0.6412    0.9849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2571   -0.6408   -0.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0039    0.8275   -0.2051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0629   -0.7449    0.7112 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  5  7  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  6 11  1  0
  6 12  1  0
  6 13  1  0
M  END
Download

3D SDF for HMDB0254610 (Methyl pyruvate)


  Mrv1533004261503042D          

  7  6  0  0  0  0            999 V2000
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0254610

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)C(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O3/c1-3(5)4(6)7-2/h1-2H3

> <INCHI_KEY>
CWKLZLBVOJRSOM-UHFFFAOYSA-N

> <FORMULA>
C4H6O3

> <MOLECULAR_WEIGHT>
102.089

> <EXACT_MASS>
102.031694053

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.40131499842363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 2-oxopropanoate

> <ALOGPS_LOGP>
-0.35

> <JCHEM_LOGP>
0.44510134266666646

> <ALOGPS_LOGS>
-0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.913251678731942

> <JCHEM_PKA_STRONGEST_BASIC>
-7.7262934720385505

> <JCHEM_POLAR_SURFACE_AREA>
43.370000000000005

> <JCHEM_REFRACTIVITY>
22.7588

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl-pyruvate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0254610 (Methyl pyruvate)

HMDB0254610
     RDKit          3D
Methyl pyruvate
 13 12  0  0  0  0  0  0  0  0999 V2000
    2.5997    0.0368    0.2670 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3215    0.3178    0.7994 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1435   -0.0301    0.1657 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2217   -0.6253   -0.9376 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1708    0.2798    0.7518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4302   -0.0948    0.0693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2274    0.8758    1.8564 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2186    0.9586    0.1573 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5390   -0.5192   -0.6975 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1083   -0.6412    0.9849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2571   -0.6408   -0.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0039    0.8275   -0.2051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0629   -0.7449    0.7112 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  5  7  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  6 11  1  0
  6 12  1  0
  6 13  1  0
M  END
Download

PDB for HMDB0254610 (Methyl pyruvate)

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  C   UNK     0       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0254610 (Methyl pyruvate)

COMPND    HMDB0254610
HETATM    1  C1  UNL     1       2.600   0.037   0.267  1.00  0.00           C  
HETATM    2  O1  UNL     1       1.322   0.318   0.799  1.00  0.00           O  
HETATM    3  C2  UNL     1       0.144  -0.030   0.166  1.00  0.00           C  
HETATM    4  O2  UNL     1       0.222  -0.625  -0.938  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.171   0.280   0.752  1.00  0.00           C  
HETATM    6  C4  UNL     1      -2.430  -0.095   0.069  1.00  0.00           C  
HETATM    7  O3  UNL     1      -1.227   0.876   1.856  1.00  0.00           O  
HETATM    8  H1  UNL     1       3.219   0.959   0.157  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.539  -0.519  -0.697  1.00  0.00           H  
HETATM   10  H3  UNL     1       3.108  -0.641   0.985  1.00  0.00           H  
HETATM   11  H4  UNL     1      -2.257  -0.641  -0.873  1.00  0.00           H  
HETATM   12  H5  UNL     1      -3.004   0.827  -0.205  1.00  0.00           H  
HETATM   13  H6  UNL     1      -3.063  -0.745   0.711  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3
CONECT    3    4    4    5
CONECT    5    6    7    7
CONECT    6   11   12   13
END
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SMILES for HMDB0254610 (Methyl pyruvate)

COC(=O)C(C)=O
Download

INCHI for HMDB0254610 (Methyl pyruvate)

InChI=1S/C4H6O3/c1-3(5)4(6)7-2/h1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Methyl 2-oxopropionateChEBI
Methylglyoxylic acid methyl esterChEBI
Pyruvic acid, methyl esterChEBI
Methyl 2-oxopropionic acidGenerator
Methylglyoxylate methyl esterGenerator
Pyruvate, methyl esterGenerator
Methyl pyruvic acidGenerator
Chemical FormulaC4H6O3
Average Molecular Weight102.089
Monoisotopic Molecular Weight102.031694053
IUPAC Namemethyl 2-oxopropanoate
Traditional Namemethyl-pyruvate
CAS Registry NumberNot Available
SMILES
COC(=O)C(C)=O
InChI Identifier
InChI=1S/C4H6O3/c1-3(5)4(6)7-2/h1-2H3
InChI KeyCWKLZLBVOJRSOM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the adjacent carbon.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassAlpha-keto acids and derivatives
Direct ParentAlpha-keto acids and derivatives
Alternative Parents
Substituents
  • Alpha-keto acid
  • Methyl ester
  • Ketone
  • Carboxylic acid ester
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.35ALOGPS
logP0.45ChemAxon
logS-0.05ALOGPS
pKa (Strongest Acidic)16.91ChemAxon
pKa (Strongest Basic)-7.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area43.37 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity22.76 m³·mol⁻¹ChemAxon
Polarizability9.4 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+124.35930932474
DeepCCS[M-H]-122.46330932474
DeepCCS[M-2H]-158.17830932474
DeepCCS[M+Na]+132.58530932474
AllCCS[M+H]+126.532859911
AllCCS[M+H-H2O]+122.232859911
AllCCS[M+NH4]+130.532859911
AllCCS[M+Na]+131.732859911
AllCCS[M-H]-123.332859911
AllCCS[M+Na-2H]-127.232859911
AllCCS[M+HCOO]-131.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Methyl pyruvateCOC(=O)C(C)=O1003.6Standard polar33892256
Methyl pyruvateCOC(=O)C(C)=O632.9Standard non polar33892256
Methyl pyruvateCOC(=O)C(C)=O702.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Methyl pyruvate,1TMS,isomer #1C=C(O[Si](C)(C)C)C(=O)OC979.7Semi standard non polar33892256
Methyl pyruvate,1TMS,isomer #1C=C(O[Si](C)(C)C)C(=O)OC978.8Standard non polar33892256
Methyl pyruvate,1TMS,isomer #1C=C(O[Si](C)(C)C)C(=O)OC1214.9Standard polar33892256
Methyl pyruvate,1TBDMS,isomer #1C=C(O[Si](C)(C)C(C)(C)C)C(=O)OC1195.0Semi standard non polar33892256
Methyl pyruvate,1TBDMS,isomer #1C=C(O[Si](C)(C)C(C)(C)C)C(=O)OC1164.9Standard non polar33892256
Methyl pyruvate,1TBDMS,isomer #1C=C(O[Si](C)(C)C(C)(C)C)C(=O)OC1393.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Methyl pyruvate GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9000000000-ba2fe2b5cbe0068337a32021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methyl pyruvate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 10V, Positive-QTOFsplash10-0udi-1900000000-6460e057db8ee4286ed02016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 20V, Positive-QTOFsplash10-0udr-9600000000-1bc512911bbaa350db7d2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 40V, Positive-QTOFsplash10-0006-9000000000-f63e1cc1d7884993bfdf2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 10V, Negative-QTOFsplash10-0udi-0900000000-e50867ebb7e3f3aeade62016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 20V, Negative-QTOFsplash10-0udi-2900000000-7fb01645be38e53936032016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 40V, Negative-QTOFsplash10-006x-9000000000-e156c58f2d39edb716922016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 10V, Positive-QTOFsplash10-0006-9000000000-6d3e39db4f0caca445d62021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 20V, Positive-QTOFsplash10-0006-9000000000-121230e371214128138c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 40V, Positive-QTOFsplash10-0006-9000000000-87bbaed151efac0845912021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 10V, Negative-QTOFsplash10-0udi-2900000000-ffb7afa029da36ade31e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 20V, Negative-QTOFsplash10-0006-9100000000-da6def5d71f7280cf6752021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl pyruvate 40V, Negative-QTOFsplash10-0006-9000000000-b201840809cda59233e72021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID11255
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethyl pyruvate
METLIN IDNot Available
PubChem Compound11748
PDB IDNot Available
ChEBI ID51850
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1260301
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]