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 .msp and .mgf format in these links:
| Format | Positive polarity | Negative polarity |
|---|---|---|
NIST .msp
|
Link | Link |
GNPS .mgf
|
Link | Link |
Installation
You can install the development version of PhenolicsDB from GitHub with:
# install.packages("devtools")
devtools::install_github("CooperstoneLab/PhenolicsDB")
library("PhenolicsDB")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.
First Batch (Agilent QTOF 6545)
| Polarity | Collision Energy (eV) |
read_dt table |
metadata table |
|---|---|---|---|
| Positive | 20 | data("read_pos20_6545") |
data("metdt_pos20_6545") |
| Positive | 40 | data("read_pos40_6545") |
data("metdt_pos40_6545") |
| Negative | 20 | data("read_neg20_6545") |
data("metdt_neg20_6545") |
| Negative | 40 | data("read_neg40_6545") |
data("metdt_neg40_6545") |
Second Batch (Agilent QTOF 6546)
| Polarity | Collision Energy (eV) |
read_dt table |
metadata table |
|---|---|---|---|
| Positive | 20 | data("read_pos20_6546") |
data("metdt_pos20_6546") |
| Positive | 40 | data("read_pos40_6546") |
data("metdt_pos40_6546") |
| Positive | 60 | data("read_pos60_6546") |
data("metdt_pos60_6546") |
| Positive | 80 | data("read_pos80_6546") |
data("metdt_pos80_6546") |
| Negative | 20 | data("read_neg20_6546") |
data("metdt_neg20_6546") |
| Negative | 40 | data("read_neg40_6546") |
data("metdt_neg40_6546") |
| Negative | 60 | data("read_neg60_6546") |
data("metdt_neg60_6546") |
| Negative | 80 | data("read_neg80_6546") |
data("metdt_neg80_6546") |
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.
Disclaimer: Metabolites with no reported data file have not MS/MS data
| Name | Formula | Monoisotopic_mass | rt (s) |
|---|---|---|---|
| 3-Hydroxybenzaldehyde | C7H6O2 | 122.0368 | 159 |
| 4-Hydroxybenzaldehyde | C7H6O2 | 122.0368 | 154 |
| Malic acid | C4H6O5 | 134.0215 | 29 |
| Salicylic acid | C7H6O3 | 138.0317 | 190 |
| D-(-)-Citramalic acid | C5H8O5 | 148.0372 | 52 |
| (E)-Cinnamic acid | C9H8O2 | 148.0524 | 221 |
| 2,4,6-Trihydroxybenzaldehyde | C7H6O4 | 154.0266 | 158 |
| 2-3-Dihydroxybenzoic acid | C7H6O4 | 154.0266 | 140 |
| 2-5-Dihydroxybenzoic acid | C7H6O4 | 154.0266 | 130 |
| 2-6-Dihydroxybenzoic acid | C7H6O4 | 154.0266 | 135 |
| 3-4-Dihydroxybenzoic acid | C7H6O4 | 154.0266 | 105 |
| Vanillyl alcohol | C8H10O3 | 154.0630 | 120 |
| p-Coumaric acid | C9H8O3 | 164.0473 | 163 |
| Vanillic acid | C8H8O4 | 168.0423 | 140 |
| Gallic acid | C7H6O5 | 170.0215 | 70 |
| Ascorbic acid | C6H8O6 | 176.0321 | 20 |
| Esculetin | C9H6O4 | 178.0266 | 142 |
| Caffeic acid | C9H8O4 | 180.0423 | 141 |
| Glucose | C6H12O6 | 180.0634 | 21 |
| D-Sorbitol | C6H14O6 | 182.0790 | 21 |
| Isoscopoletin | C10H8O4 | 192.0423 | 168 |
| Scopoletin | C10H8O4 | 192.0423 | 173 |
| Quinic acid | C7H12O6 | 192.0634 | 22 |
| Ferrulic acid | C10H10O4 | 194.0579 | 172 |
| Sinapic acid | C11H12O5 | 224.0685 | 174 |
| Apigenin | C15H10O5 | 270.0528 | 236 |
| Naringenin | C15H12O5 | 272.0685 | 183 |
| Phloretin | C15H14O5 | 274.0841 | 236 |
| Fisetin | C15H10O6 | 286.0477 | 197 |
| Kaempferol | C15H10O6 | 286.0477 | 242 |
| (-)-Epicatechin | C15H14O6 | 290.0790 | 142 |
| Catechin | C15H14O6 | 290.0790 | 132 |
| Kaempferide | C16H12O6 | 300.0634 | 293 |
| Ellagic acid | C14H6O8 | 302.0063 | 172 |
| Herbacetin | C15H10O7 | 302.0427 | 212 |
| Quercetin | C15H10O7 | 302.0427 | 220 |
| 3-O-methyl Quercetin | C16H12O7 | 316.0583 | 224 |
| Isorhamnetin | C16H12O7 | 316.0583 | 246 |
| Tamarixetin | C16H12O7 | 316.0583 | 245 |
| Sucrose | C12H22O11 | 342.1162 | 25 |
| Chlorogenic acid | C16H18O9 | 354.0951 | 135 |
| Cryptochlorogenic acid | C16H18O9 | 354.0951 | 136 |
| Neochlorogenic acid | C16H18O9 | 354.0951 | 120 |
| Avicularin | C20H18O11 | 434.0849 | 178 |
| Guaijaverin | C20H18O11 | 434.0849 | 179 |
| Phloridzin | C21H24O10 | 436.1369 | 191 |
| Trilobatin | C21H24O10 | 436.1369 | 201 |
| Astragalin | C21H20O11 | 448.1006 | 182 |
| Quercitrin | C21H20O11 | 448.1006 | 182 |
| Cyanidin 3-Galactoside | C21H21O11 | 449.1084 | 128 |
| Eriodictyol 7-O-glucoside | C21H22O11 | 450.1162 | 169 |
| Ursolic acid | C30H48O3 | 456.3603 | 434 |
| Isoquercitrin | C21H20O12 | 464.0955 | 174 |
| Isoquercitroside | C21H20O12 | 464.0955 | 170 |
| Quercetin-3-galactoside | C21H20O12 | 464.0955 | 174 |
| Quercetin-3-glucoside | C21H20O12 | 464.0955 | 174 |
| Corosolic acid | C30H48O4 | 472.3553 | 371 |
| Quercetin-3-O-glucuronide | C21H18O13 | 478.0747 | 172 |
| Melezitose | C18H32O16 | 504.1690 | 24 |
| Procyanidin A2 | C30H24O12 | 576.1268 | 172 |
| Procyanidin B1 | C30H26O12 | 578.1424 | 118 |
| Procyanidin B2 | C30H26O12 | 578.1424 | 139 |
| Procyanidin B3 | C30H26O12 | 578.1424 | 124 |
| Naringin | C27H32O14 | 580.1792 | 182 |
| Procyanidin | C30H26O13 | 594.1373 | 160 |
| Nictoflorin | C27H30O15 | 594.1585 | 178 |
| Saponarin | C27H30O15 | 594.1585 | 151 |
| Eriocitrin | C27H32O15 | 596.1741 | 166 |
| Neoeriocitrin | C27H32O15 | 596.1741 | 168 |
| Rutin | C27H30O16 | 610.1534 | 166 |
| Narcissin | C28H32O16 | 624.1690 | 180 |
| Quercetin 3-O-sophoroside | C27H30O17 | 626.1483 | 154 |
| Procyanidin C1 | C45H38O18 | 866.2058 | 146 |
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/},
#> }