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PhenolicsDB

PhenolicsDB is a data package that contains raw MS/MS data of authentic analytical standards. PhenolicsDB raw data files and data frames are aimed to exemplify the use of MS2extract to create in-house metabolite MS/MS libraries. Between the list of metabolites we include phenolic acids, flavonoids, dihydrochalcones, carbohydrates, and others. Tandem mass spectrometry data was collected using a LC coupled to a Q-TOF mass analyzer.

Download PhenolicsDB

You can download PhenolicsDB in these links:

You can also access the .mzML files used for this library in the following link

Database description

This package is intended to archive the raw .mzML files of authentic analytical standards, as well as structured data frames aimed to be used jointly with MS2extract, to automate the process of creating in-house MS/MS libraries.

This database contains majorly phenolics compounds, aimed to decipher and annotate the Rosacea metabolome. However, as phenolics are expressed in a wide range of organisms, this database can be used in multiple scenarios.

We grouped the total database in two batches. The batches are based on the instrument we used to acquire the MS/MS data. For the first batch, we used an Agilent QTOF 6545, and for the second batch, we used an Agilent QTOF 6546. In both batches, we collected targeted MS/MS using the chromatographic method reported in Bilbrey at al. (2022). We collected data in negative and positive polarity, and we used 20 and 40 eV (CE) using collision induced dissociation (CID). Additionally, in the second batch, we also collected data at 60 and 80 eV (CE). The following tables describe the set of data frames that you can load and use with MS2extract.

List of metabolites

In the extdata directory you will find all the .mzML files for all standards, as well as the structure tables to be used jointly with MS2extract.

In the following table you can see the list of metabolites we are including in this version of the database, as well as in what batch you will find them.

MS/MS spectra included in this library can be viewed here

Name Formula Ionization_mode rt (min) Collision Energy Monoisotopic_mass
2,3-Dihydroxybenzoic acid C7H6O4 Negative 2.342 20 eV, 40 eV 154.0266
2,3-Dihydroxybenzoic acid C7H6O4 Positive 2.342 20 eV, 40 eV 154.0266
2,4,6-Trihydroxybenzaldehyde C7H6O4 Negative 2.625 20 eV, 40 eV 154.0266
2,4,6-Trihydroxybenzaldehyde C7H6O4 Positive 2.625 20 eV, 40 eV 154.0266
2,5-Dihydroxybenzoic acid C7H6O4 Negative 2.167 20 eV, 40 eV 154.0266
2,5-Dihydroxybenzoic acid C7H6O4 Positive 2.167 20 eV, 40 eV 154.0266
2,6-Dihydroxybenzoic acid C7H6O4 Negative 2.250 20 eV, 40 eV 154.0266
2,6-Dihydroxybenzoic acid C7H6O4 Positive 2.250 20 eV, 40 eV 154.0266
3’-O-Methyl quercetin C16H12O7 Negative 4.100 20 eV, 40 eV 316.0583
3’-O-Methyl quercetin C16H12O7 Positive 4.100 20 eV, 40 eV 316.0583
3,4-Dihydroxybenzoic acid C7H6O4 Negative 1.750 20 eV, 40 eV 154.0266
3,4-Dihydroxybenzoic acid C7H6O4 Positive 1.750 20 eV, 40 eV 154.0266
3-Hydroxybenzaldehyde C7H6O2 Negative 2.650 20 eV, 40 eV 122.0368
3-Hydroxybenzaldehyde C7H6O2 Positive 2.650 20 eV, 40 eV 122.0368
3-O-Caffeoylquinic acid (IUPAC) C16H18O9 Negative 2.000 20 eV, 40 eV, 60 eV, 80 eV 354.0951
3-O-Caffeoylquinic acid (IUPAC) C16H18O9 Positive 2.000 20 eV, 40 eV 354.0951
3-O-methyl Quercetin C16H12O7 Negative 3.725 20 eV, 40 eV, 60 eV, 80 eV 316.0583
3-O-methyl Quercetin C16H12O7 Positive 3.725 20 eV, 40 eV, 60 eV, 80 eV 316.0583
4’-O-Methyl quercetin C16H12O7 Negative 4.083 20 eV, 40 eV, 60 eV, 80 eV 316.0583
4’-O-Methyl quercetin C16H12O7 Positive 4.083 20 eV, 40 eV, 60 eV, 80 eV 316.0583
4-Hydroxybenzaldehyde C7H6O2 Negative 2.558 20 eV, 40 eV 122.0368
4-Hydroxybenzaldehyde C7H6O2 Positive 2.558 20 eV 122.0368
4-O-Caffeoylquinic acid (IUPAC) C16H18O9 Negative 2.258 20 eV, 40 eV, 60 eV, 80 eV 354.0951
4-O-Caffeoylquinic acid (IUPAC) C16H18O9 Positive 2.258 20 eV, 40 eV 354.0951
4prime-O-Methyl kaempferol C16H12O6 Negative 4.883 20 eV, 40 eV 300.0634
4prime-O-Methyl kaempferol C16H12O6 Positive 4.883 20 eV, 40 eV 300.0634
5-O-Caffeoylquinic acid (IUPAC) C16H18O9 Negative 2.250 20 eV, 40 eV, 60 eV, 80 eV 354.0951
5-O-Caffeoylquinic acid (IUPAC) C16H18O9 Positive 2.250 20 eV, 40 eV 354.0951
6,7-Dihydroxycoumarin C9H6O4 Negative 2.375 20 eV, 40 eV, 60 eV, 80 eV 178.0266
6,7-Dihydroxycoumarin C9H6O4 Positive 2.375 20 eV, 40 eV, 60 eV, 80 eV 178.0266
6-Hydroxy-7-methoxycoumarin C10H8O4 Negative 2.792 20 eV, 40 eV, 60 eV, 80 eV 192.0423
6-Hydroxy-7-methoxycoumarin C10H8O4 Positive 2.792 20 eV, 40 eV, 60 eV, 80 eV 192.0423
Apigenin C15H10O5 Negative 3.942 20 eV, 40 eV, 60 eV, 80 eV 270.0528
Apigenin C15H10O5 Positive 3.942 20 eV, 40 eV, 60 eV, 80 eV 270.0528
Ascorbic acid C6H8O6 Negative 0.333 20 eV, 40 eV 176.0321
Ascorbic acid C6H8O6 Positive 0.333 20 eV, 40 eV 176.0321
Caffeic acid C9H8O4 Negative 2.350 20 eV, 40 eV 180.0423
Caffeic acid C9H8O4 Positive 2.350 20 eV, 40 eV 180.0423
Catechin C15H14O6 Negative 2.208 20 eV, 40 eV 290.0790
Catechin C15H14O6 Positive 2.208 20 eV, 40 eV 290.0790
Cinnamic acid C9H8O2 Negative 3.683 20 eV, 40 eV 148.0524
Cinnamic acid C9H8O2 Positive 3.683 20 eV, 40 eV 148.0524
Citramalic acid C5H8O5 Negative 0.875 20 eV, 40 eV, 60 eV, 80 eV 148.0372
Corosolic acid C30H48O4 Negative 6.183 20 eV 472.3553
Corosolic acid C30H48O4 Positive 6.183 20 eV 472.3553
Cyanidin 3-O-galactoside C21H21O11 Negative 2.125 20 eV, 40 eV, 60 eV, 80 eV 449.1084
Ellagic acid C14H6O8 Negative 2.875 20 eV, 40 eV 302.0063
Ellagic acid C14H6O8 Positive 2.875 20 eV, 40 eV 302.0063
Epicatechin C15H14O6 Negative 2.375 20 eV, 40 eV 290.0790
Epicatechin C15H14O6 Positive 2.375 20 eV, 40 eV 290.0790
Eriodictyol 7-O-glucoside C21H22O11 Negative 2.817 20 eV, 40 eV, 60 eV, 80 eV 450.1162
Eriodictyol 7-O-glucoside C21H22O11 Positive 2.817 20 eV, 40 eV, 60 eV, 80 eV 450.1162
Eriodictyol 7-O-neohesperidoside C27H32O15 Negative 2.808 20 eV, 40 eV 596.1741
Eriodictyol 7-O-neohesperidoside C27H32O15 Positive 2.808 20 eV, 40 eV 596.1741
Eriodictyol 7-O-rutinoside C27H32O15 Negative 2.767 20 eV, 40 eV 596.1741
Eriodictyol 7-O-rutinoside C27H32O15 Positive 2.767 20 eV, 40 eV 596.1741
Ferulic acid C10H10O4 Negative 2.867 20 eV, 40 eV 194.0579
Ferulic acid C10H10O4 Positive 2.867 20 eV, 40 eV 194.0579
Fisetin C15H10O6 Negative 3.283 20 eV, 40 eV 286.0477
Fisetin C15H10O6 Positive 3.283 20 eV, 40 eV 286.0477
Gallic acid C7H6O5 Negative 1.167 20 eV, 40 eV 170.0215
Gallic acid C7H6O5 Positive 1.167 20 eV, 40 eV 170.0215
Glucose C6H12O6 Negative 0.350 20 eV 180.0634
Herbacetin C15H10O7 Negative 3.525 20 eV, 40 eV 302.0427
Herbacetin C15H10O7 Positive 3.525 20 eV, 40 eV 302.0427
Isoquercitroside C21H20O12 Negative 2.833 20 eV, 40 eV 464.0955
Isoquercitroside C21H20O12 Positive 2.833 20 eV, 40 eV 464.0955
Isorhamnetin 3-O-rutinoside C28H32O16 Negative 3.000 20 eV, 40 eV 624.1690
Isorhamnetin 3-O-rutinoside C28H32O16 Positive 3.000 20 eV, 40 eV 624.1690
Kaempferol C15H10O6 Negative 4.042 20 eV, 40 eV 286.0477
Kaempferol C15H10O6 Positive 4.042 20 eV, 40 eV 286.0477
Kaempferol 3-O-glucoside C21H20O11 Negative 3.025 20 eV, 40 eV 448.1006
Kaempferol 3-O-glucoside C21H20O11 Positive 3.025 20 eV, 40 eV 448.1006
Kaempferol 3-O-rutinoside C27H30O15 Negative 2.958 20 eV, 40 eV 594.1585
Kaempferol 3-O-rutinoside C27H30O15 Positive 2.958 20 eV, 40 eV 594.1585
Malic acid C4H6O5 Negative 0.483 20 eV 134.0215
Melezitose C18H32O16 Negative 0.400 20 eV, 40 eV 504.1690
Melezitose C18H32O16 Positive 0.400 20 eV, 40 eV 504.1690
Naringenin C15H12O5 Negative 3.050 20 eV, 40 eV 272.0685
Naringenin C15H12O5 Positive 3.050 20 eV, 40 eV 272.0685
Naringin C27H32O14 Negative 3.042 20 eV, 40 eV 580.1792
Naringin C27H32O14 Positive 3.042 20 eV, 40 eV 580.1792
Phloretin C15H14O5 Negative 3.933 20 eV, 40 eV 274.0841
Phloretin C15H14O5 Positive 3.933 20 eV, 40 eV 274.0841
Phloridzin C21H24O10 Negative 3.183 20 eV, 40 eV 436.1369
Phloridzin C21H24O10 Positive 3.183 20 eV, 40 eV 436.1369
Procyanidin C30H26O13 Negative 2.667 20 eV, 40 eV 594.1373
Procyanidin C30H26O13 Positive 2.667 20 eV, 40 eV 594.1373
Procyanidin A2 C30H24O12 Negative 2.858 20 eV, 40 eV 576.1268
Procyanidin A2 C30H24O12 Positive 2.858 20 eV, 40 eV 576.1268
Procyanidin B1 C30H26O12 Negative 1.958 20 eV, 40 eV 578.1424
Procyanidin B1 C30H26O12 Positive 1.958 20 eV, 40 eV 578.1424
Procyanidin B2 C30H26O12 Negative 2.317 20 eV, 40 eV 578.1424
Procyanidin B2 C30H26O12 Positive 2.317 20 eV, 40 eV 578.1424
Procyanidin B3 C30H26O12 Negative 2.075 20 eV, 40 eV 578.1424
Procyanidin B3 C30H26O12 Positive 2.075 20 eV, 40 eV 578.1424
Procyanidin C1 C45H38O18 Negative 2.433 20 eV, 40 eV 866.2058
Procyanidin C1 C45H38O18 Positive 2.433 20 eV, 40 eV 866.2058
Quercetin C15H10O7 Negative 3.658 40 eV 302.0427
Quercetin C15H10O7 Positive 3.658 40 eV 302.0427
Quercetin 3-O-arabinofuranoside C20H18O11 Negative 2.975 20 eV, 40 eV, 60 eV, 80 eV 434.0849
Quercetin 3-O-arabinofuranoside C20H18O11 Positive 2.975 20 eV, 40 eV, 60 eV, 80 eV 434.0849
Quercetin 3-O-arabinopyranoside C20H18O11 Negative 2.983 20 eV, 40 eV, 60 eV, 80 eV 434.0849
Quercetin 3-O-arabinopyranoside C20H18O11 Positive 2.983 20 eV, 40 eV, 60 eV, 80 eV 434.0849
Quercetin 3-O-galactoside C21H20O12 Negative 2.892 40 eV 464.0955
Quercetin 3-O-galactoside C21H20O12 Positive 2.892 40 eV 464.0955
Quercetin 3-O-glucofuranoside C21H20O12 Negative 2.892 20 eV, 40 eV 464.0955
Quercetin 3-O-glucofuranoside C21H20O12 Positive 2.892 20 eV, 40 eV 464.0955
Quercetin 3-O-glucoside C21H20O12 Negative 2.892 20 eV, 40 eV 464.0955
Quercetin 3-O-glucoside C21H20O12 Positive 2.892 20 eV, 40 eV 464.0955
Quercetin 3-O-glucuronide C21H18O13 Negative 2.875 20 eV, 40 eV 478.0747
Quercetin 3-O-glucuronide C21H18O13 Positive 2.875 20 eV, 40 eV 478.0747
Quercetin 3-O-rhamnoside C21H20O11 Negative 3.042 20 eV, 40 eV 448.1006
Quercetin 3-O-rhamnoside C21H20O11 Positive 3.042 20 eV, 40 eV 448.1006
Quercetin 3-O-rutinoside C27H30O16 Negative 2.775 20 eV, 40 eV 610.1534
Quercetin 3-O-rutinoside C27H30O16 Positive 2.775 20 eV, 40 eV 610.1534
Quercetin 3-O-sophoroside C27H30O17 Negative 2.575 40 eV 626.1483
Quercetin 3-O-sophoroside C27H30O17 Positive 2.575 20 eV, 40 eV 626.1483
Quinic acid C7H12O6 Negative 0.358 20 eV, 40 eV 192.0634
Quinic acid C7H12O6 Positive 0.358 20 eV, 40 eV 192.0634
Salicylic acid C7H6O3 Negative 3.167 20 eV 138.0317
Salicylic acid C7H6O3 Positive 3.167 20 eV, 40 eV 138.0317
Saponaretin 7-O-glucoside C27H30O15 Negative 2.517 20 eV, 40 eV, 60 eV, 80 eV 594.1585
Saponaretin 7-O-glucoside C27H30O15 Positive 2.517 20 eV, 40 eV, 60 eV, 80 eV 594.1585
Scopoletin C10H8O4 Negative 2.883 20 eV, 40 eV, 60 eV, 80 eV 192.0423
Scopoletin C10H8O4 Positive 2.883 20 eV, 40 eV, 60 eV, 80 eV 192.0423
Sinapic acid C11H12O5 Negative 2.908 20 eV, 40 eV 224.0685
Sinapic acid C11H12O5 Positive 2.908 20 eV, 40 eV 224.0685
Sorbitol C6H14O6 Negative 0.350 20 eV, 40 eV 182.0790
Sorbitol C6H14O6 Positive 0.350 20 eV, 40 eV 182.0790
Sucrose C12H22O11 Negative 0.417 20 eV, 40 eV 342.1162
Sucrose C12H22O11 Positive 0.417 20 eV, 40 eV 342.1162
Ursolic acid C30H48O3 Negative 7.233 20 eV, 40 eV 456.3603
Vanillic acid C8H8O4 Negative 2.342 20 eV, 40 eV 168.0423
Vanillic acid C8H8O4 Positive 2.342 20 eV, 40 eV 168.0423
Vanillyl alcohol C8H10O3 Negative 2.000 20 eV 154.0630
Vanillyl alcohol C8H10O3 Positive 2.000 20 eV, 40 eV 154.0630
p-Coumaric acid C9H8O3 Negative 2.717 20 eV, 40 eV 164.0473
p-Coumaric acid C9H8O3 Positive 2.717 20 eV, 40 eV 164.0473
phloretin 4’-O-glucoside C21H24O10 Negative 3.350 20 eV, 40 eV 436.1369
phloretin 4’-O-glucoside C21H24O10 Positive 3.350 20 eV, 40 eV 436.1369

Citing PhenolicsDB

To cite PhenolicsDB in your publications, please use:

## Citation info
citation("PhenolicsDB")
#> To cite PhenolicsDB in publications use:
#> 
#>   Quiroz-Moreno C, Cooperstone J (2023). _PhenolicsDB: phenolics MS/MS
#>   (LC-ESI-QTOF) database repository_. doi:10.5281/zenodo.8475
#>   <https://doi.org/10.5281/zenodo.8475>,
#>   <https://cooperstonelab.github.io/PhenolicsDB/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {PhenolicsDB: phenolics MS/MS (LC-ESI-QTOF) database repository},
#>     author = {Cristian Quiroz-Moreno and Jessica Cooperstone},
#>     year = {2023},
#>     doi = {10.5281/zenodo.8475},
#>     url = {https://cooperstonelab.github.io/PhenolicsDB/},
#>   }