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:

Negative polarity (link)
Positive polarity (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
2,3-Dihydroxybenzoic acid	C7H6O4	Negative	2.342	20 eV, 40 eV
2,3-Dihydroxybenzoic acid	C7H6O4	Positive	2.342	20 eV, 40 eV
2,4,6-Trihydroxybenzaldehyde	C7H6O4	Negative	2.625	20 eV, 40 eV
2,4,6-Trihydroxybenzaldehyde	C7H6O4	Positive	2.625	20 eV, 40 eV
2,5-Dihydroxybenzoic acid	C7H6O4	Negative	2.167	20 eV, 40 eV
2,5-Dihydroxybenzoic acid	C7H6O4	Positive	2.167	20 eV, 40 eV
2,6-Dihydroxybenzoic acid	C7H6O4	Negative	2.250	20 eV, 40 eV
2,6-Dihydroxybenzoic acid	C7H6O4	Positive	2.250	20 eV, 40 eV
3,4-Dihydroxybenzoic acid	C7H6O4	Negative	1.750	20 eV, 40 eV
3,4-Dihydroxybenzoic acid	C7H6O4	Positive	1.750	20 eV, 40 eV
3-Hydroxybenzaldehyde	C7H6O2	Negative	2.650	20 eV, 40 eV
3-Hydroxybenzaldehyde	C7H6O2	Positive	2.650	20 eV, 40 eV
3-O-Caffeoylquinic acid (IUPAC)	C16H18O9	Negative	2.000	20 eV, 40 eV, 60 eV, 80 eV
3-O-Caffeoylquinic acid (IUPAC)	C16H18O9	Positive	2.000	20 eV, 40 eV
3-O-Methyl quercetin	C16H12O7	Negative	4.100	20 eV, 40 eV
3-O-Methyl quercetin	C16H12O7	Positive	4.100	20 eV, 40 eV
3-O-methyl Quercetin	C16H12O7	Negative	3.725	20 eV, 40 eV, 60 eV, 80 eV
3-O-methyl Quercetin	C16H12O7	Positive	3.725	20 eV, 40 eV, 60 eV, 80 eV
4-Hydroxybenzaldehyde	C7H6O2	Negative	2.558	20 eV, 40 eV
4-Hydroxybenzaldehyde	C7H6O2	Positive	2.558	20 eV
4-O-Caffeoylquinic acid (IUPAC)	C16H18O9	Negative	2.258	20 eV, 40 eV, 60 eV, 80 eV
4-O-Caffeoylquinic acid (IUPAC)	C16H18O9	Positive	2.258	20 eV, 40 eV
4prime-O-Methyl kaempferol	C16H12O6	Negative	4.883	20 eV, 40 eV
4prime-O-Methyl kaempferol	C16H12O6	Positive	4.883	20 eV, 40 eV
4prime-O-Methyl quercetin	C16H12O7	Negative	4.083	20 eV, 40 eV, 60 eV, 80 eV
4prime-O-Methyl quercetin	C16H12O7	Positive	4.083	20 eV, 40 eV, 60 eV, 80 eV
5-O-Caffeoylquinic acid (IUPAC)	C16H18O9	Negative	2.250	20 eV, 40 eV, 60 eV, 80 eV
5-O-Caffeoylquinic acid (IUPAC)	C16H18O9	Positive	2.250	20 eV, 40 eV
6,7-Dihydroxycoumarin	C9H6O4	Negative	2.375	20 eV, 40 eV, 60 eV, 80 eV
6,7-Dihydroxycoumarin	C9H6O4	Positive	2.375	20 eV, 40 eV, 60 eV, 80 eV
6-Hydroxy-7-methoxycoumarin	C10H8O4	Negative	2.792	20 eV, 40 eV, 60 eV, 80 eV
6-Hydroxy-7-methoxycoumarin	C10H8O4	Positive	2.792	20 eV, 40 eV, 60 eV, 80 eV
Apigenin	C15H10O5	Negative	3.942	20 eV, 40 eV, 60 eV, 80 eV
Apigenin	C15H10O5	Positive	3.942	20 eV, 40 eV, 60 eV, 80 eV
Ascorbic acid	C6H8O6	Negative	0.333	20 eV, 40 eV
Ascorbic acid	C6H8O6	Positive	0.333	20 eV, 40 eV
Caffeic acid	C9H8O4	Negative	2.350	20 eV, 40 eV
Caffeic acid	C9H8O4	Positive	2.350	20 eV, 40 eV
Catechin	C15H14O6	Negative	2.208	20 eV, 40 eV
Catechin	C15H14O6	Positive	2.208	20 eV, 40 eV
Cinnamic acid	C9H8O2	Negative	3.683	20 eV, 40 eV
Cinnamic acid	C9H8O2	Positive	3.683	20 eV, 40 eV
Citramalic acid	C5H8O5	Negative	0.875	20 eV, 40 eV, 60 eV, 80 eV
Corosolic acid	C30H48O4	Negative	6.183	20 eV
Corosolic acid	C30H48O4	Positive	6.183	20 eV
Cyanidin 3-O-galactoside	C21H21O11	Negative	2.125	20 eV, 40 eV, 60 eV, 80 eV
Ellagic acid	C14H6O8	Negative	2.875	20 eV, 40 eV
Ellagic acid	C14H6O8	Positive	2.875	20 eV, 40 eV
Epicatechin	C15H14O6	Negative	2.375	20 eV, 40 eV
Epicatechin	C15H14O6	Positive	2.375	20 eV, 40 eV
Eriodictyol 7-O-glucoside	C21H22O11	Negative	2.817	20 eV, 40 eV, 60 eV, 80 eV
Eriodictyol 7-O-glucoside	C21H22O11	Positive	2.817	20 eV, 40 eV, 60 eV, 80 eV
Eriodictyol 7-O-neohesperidoside	C27H32O15	Negative	2.808	20 eV, 40 eV
Eriodictyol 7-O-neohesperidoside	C27H32O15	Positive	2.808	20 eV, 40 eV
Eriodictyol 7-O-rutinoside	C27H32O15	Negative	2.767	20 eV, 40 eV
Eriodictyol 7-O-rutinoside	C27H32O15	Positive	2.767	20 eV, 40 eV
Ferulic acid	C10H10O4	Negative	2.867	20 eV, 40 eV
Ferulic acid	C10H10O4	Positive	2.867	20 eV, 40 eV
Fisetin	C15H10O6	Negative	3.283	20 eV, 40 eV
Fisetin	C15H10O6	Positive	3.283	20 eV, 40 eV
Gallic acid	C7H6O5	Negative	1.167	20 eV, 40 eV
Gallic acid	C7H6O5	Positive	1.167	20 eV, 40 eV
Glucose	C6H12O6	Negative	0.350	20 eV
Herbacetin	C15H10O7	Negative	3.525	20 eV, 40 eV
Herbacetin	C15H10O7	Positive	3.525	20 eV, 40 eV
Isoquercitroside	C21H20O12	Negative	2.833	20 eV, 40 eV
Isoquercitroside	C21H20O12	Positive	2.833	20 eV, 40 eV
Isorhamnetin 3-O-rutinoside	C28H32O16	Negative	3.000	20 eV, 40 eV
Isorhamnetin 3-O-rutinoside	C28H32O16	Positive	3.000	20 eV, 40 eV
Kaempferol	C15H10O6	Negative	4.042	20 eV, 40 eV
Kaempferol	C15H10O6	Positive	4.042	20 eV, 40 eV
Kaempferol 3-O-glucoside	C21H20O11	Negative	3.025	20 eV, 40 eV
Kaempferol 3-O-glucoside	C21H20O11	Positive	3.025	20 eV, 40 eV
Kaempferol 3-O-rutinoside	C27H30O15	Negative	2.958	20 eV, 40 eV
Kaempferol 3-O-rutinoside	C27H30O15	Positive	2.958	20 eV, 40 eV
Malic acid	C4H6O5	Negative	0.483	20 eV
Melezitose	C18H32O16	Negative	0.400	20 eV, 40 eV
Melezitose	C18H32O16	Positive	0.400	20 eV, 40 eV
Naringenin	C15H12O5	Negative	3.050	20 eV, 40 eV
Naringenin	C15H12O5	Positive	3.050	20 eV, 40 eV
Naringin	C27H32O14	Negative	3.042	20 eV, 40 eV
Naringin	C27H32O14	Positive	3.042	20 eV, 40 eV
Phloretin	C15H14O5	Negative	3.933	20 eV, 40 eV
Phloretin	C15H14O5	Positive	3.933	20 eV, 40 eV
Phloridzin	C21H24O10	Negative	3.183	20 eV, 40 eV
Phloridzin	C21H24O10	Positive	3.183	20 eV, 40 eV
Procyanidin	C30H26O13	Negative	2.667	20 eV, 40 eV
Procyanidin	C30H26O13	Positive	2.667	20 eV, 40 eV
Procyanidin A2	C30H24O12	Negative	2.858	20 eV, 40 eV
Procyanidin A2	C30H24O12	Positive	2.858	20 eV, 40 eV
Procyanidin B1	C30H26O12	Negative	1.958	20 eV, 40 eV
Procyanidin B1	C30H26O12	Positive	1.958	20 eV, 40 eV
Procyanidin B2	C30H26O12	Negative	2.317	20 eV, 40 eV
Procyanidin B2	C30H26O12	Positive	2.317	20 eV, 40 eV
Procyanidin B3	C30H26O12	Negative	2.075	20 eV, 40 eV
Procyanidin B3	C30H26O12	Positive	2.075	20 eV, 40 eV
Procyanidin C1	C45H38O18	Negative	2.433	20 eV, 40 eV
Procyanidin C1	C45H38O18	Positive	2.433	20 eV, 40 eV
Quercetin	C15H10O7	Negative	3.658	40 eV
Quercetin	C15H10O7	Positive	3.658	40 eV
Quercetin 3-O-arabinofuranoside	C20H18O11	Negative	2.975	20 eV, 40 eV, 60 eV, 80 eV
Quercetin 3-O-arabinofuranoside	C20H18O11	Positive	2.975	20 eV, 40 eV, 60 eV, 80 eV
Quercetin 3-O-arabinopyranoside	C20H18O11	Negative	2.983	20 eV, 40 eV, 60 eV, 80 eV
Quercetin 3-O-arabinopyranoside	C20H18O11	Positive	2.983	20 eV, 40 eV, 60 eV, 80 eV
Quercetin 3-O-galactoside	C21H20O12	Negative	2.892	40 eV
Quercetin 3-O-galactoside	C21H20O12	Positive	2.892	40 eV
Quercetin 3-O-glucofuranoside	C21H20O12	Negative	2.892	20 eV, 40 eV
Quercetin 3-O-glucofuranoside	C21H20O12	Positive	2.892	20 eV, 40 eV
Quercetin 3-O-glucoside	C21H20O12	Negative	2.892	20 eV, 40 eV
Quercetin 3-O-glucoside	C21H20O12	Positive	2.892	20 eV, 40 eV
Quercetin 3-O-glucuronide	C21H18O13	Negative	2.875	20 eV, 40 eV
Quercetin 3-O-glucuronide	C21H18O13	Positive	2.875	20 eV, 40 eV
Quercetin 3-O-rhamnoside	C21H20O11	Negative	3.042	20 eV, 40 eV
Quercetin 3-O-rhamnoside	C21H20O11	Positive	3.042	20 eV, 40 eV
Quercetin 3-O-rutinoside	C27H30O16	Negative	2.775	20 eV, 40 eV
Quercetin 3-O-rutinoside	C27H30O16	Positive	2.775	20 eV, 40 eV
Quercetin 3-O-sophoroside	C27H30O17	Negative	2.575	40 eV
Quercetin 3-O-sophoroside	C27H30O17	Positive	2.575	20 eV, 40 eV
Quinic acid	C7H12O6	Negative	0.358	20 eV, 40 eV
Quinic acid	C7H12O6	Positive	0.358	20 eV, 40 eV
Salicylic acid	C7H6O3	Negative	3.167	20 eV
Salicylic acid	C7H6O3	Positive	3.167	20 eV, 40 eV
Saponaretin 7-O-glucoside	C27H30O15	Negative	2.517	20 eV, 40 eV, 60 eV, 80 eV
Saponaretin 7-O-glucoside	C27H30O15	Positive	2.517	20 eV, 40 eV, 60 eV, 80 eV
Scopoletin	C10H8O4	Negative	2.883	20 eV, 40 eV, 60 eV, 80 eV
Scopoletin	C10H8O4	Positive	2.883	20 eV, 40 eV, 60 eV, 80 eV
Sinapic acid	C11H12O5	Negative	2.908	20 eV, 40 eV
Sinapic acid	C11H12O5	Positive	2.908	20 eV, 40 eV
Sorbitol	C6H14O6	Negative	0.350	20 eV, 40 eV
Sorbitol	C6H14O6	Positive	0.350	20 eV, 40 eV
Sucrose	C12H22O11	Negative	0.417	20 eV, 40 eV
Sucrose	C12H22O11	Positive	0.417	20 eV, 40 eV
Trilobatin	C21H24O10	Negative	3.350	20 eV, 40 eV
Trilobatin	C21H24O10	Positive	3.350	20 eV, 40 eV
Ursolic acid	C30H48O3	Negative	7.233	20 eV, 40 eV
Vanillic acid	C8H8O4	Negative	2.342	20 eV, 40 eV
Vanillic acid	C8H8O4	Positive	2.342	20 eV, 40 eV
Vanillyl alcohol	C8H10O3	Negative	2.000	20 eV
Vanillyl alcohol	C8H10O3	Positive	2.000	20 eV, 40 eV
p-Coumaric acid	C9H8O3	Negative	2.717	20 eV, 40 eV
p-Coumaric acid	C9H8O3	Positive	2.717	20 eV, 40 eV

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/},
#>   }

PhenolicsDB

Download PhenolicsDB

Database description

List of metabolites

Citing PhenolicsDB

Citing `PhenolicsDB`