2 - Content description of the Phenolics MS/MS repository • PhenolicsDB

Package content 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 phenolic compounds, aimed to decipher and annotate the Rosacea metabolome. However, as phenolics are expressed almost ubiquitously in plants, this database can be used in multiples scenarios where researchers rationalize PhenolicsDB could help to annotate metabolites present in their dataset.

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 the 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).

Again, this data package is intended to work with MS2extract, as its structure meets the requirements in MS2extract, where the read_dt tables enable importing the .mzML files, while the met_metadata has crucial information that is included in the final MS/MS library.

First Batch (Agilent QTOF 6545)

Polarity	Collision Energy (eV)	read_dt table	met_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")`

PhenolicsDB metadata for GNPS `.mgf` format

You can also use the metdt_GNPS_pos and metdt_GNPS_pos data frames to export this library in a .mgf format.

List of metabolites

In the extdata directory you will find all the .mzML files for all the 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

Metabolites in two dimensions

As it was explained above, the chromatography method employed for the LC separation is described in Bilbrey at al. (2022).

Therefore, we can display where each metabolite elutes in terms of retention time and m/z.

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Bibliography

This vignette was generated using BiocStyle (Oleś, 2023) with knitr (Xie, 2023) and rmarkdown (Allaire, Xie, Dervieux, McPherson, Luraschi, Ushey, Atkins, Wickham, Cheng, Chang, and Iannone, 2023) running behind the scenes.

Citations made with RefManageR (McLean, 2017).

[1] J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents for R. R package version 2.25. 2023. URL: https://github.com/rstudio/rmarkdown.

[2] M. W. McLean. “RefManageR: Import and Manage BibTeX and BibLaTeX References in R”. In: The Journal of Open Source Software (2017). DOI: 10.21105/joss.00338.

[3] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.30.0. 2023. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle.

[4] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.45. 2023. URL: https://yihui.org/knitr/.

2 - Content description of the Phenolics MS/MS repository

Cristian Quiroz-Moreno, Jessica Coopestone

3 February 2024

Package content description

First Batch (Agilent QTOF 6545)

Second Batch (Agilent QTOF 6546)

PhenolicsDB metadata for GNPS `.mgf` format

List of metabolites

Metabolites in two dimensions

Information about this vignette

Bibliography

2 - Content description of the Phenolics MS/MS repository

Cristian Quiroz-Moreno, Jessica Coopestone

3 February 2024

Package content description

First Batch (Agilent QTOF 6545)

Second Batch (Agilent QTOF 6546)

PhenolicsDB metadata for GNPS .mgf format

List of metabolites

Metabolites in two dimensions

Information about this vignette

Bibliography

PhenolicsDB metadata for GNPS `.mgf` format