pgf2- alpha

[JuliaCovic]

ACCESSION: MSBNK-MIYAMOTOLAB_USP
RECORD_TITLE: PGF2a; LC-ESI-QFT; MS2; CE: unknown; R=30.000; [M-H]-
DATE: 2025.04.24
AUTHORS: Julia Rosangela Sayuri MIYAMITOLAB_USP
LICENSE: CC BY
COPYRIGHT: Copyright (C) 2025, USP
COMMENT: Sample acquired via negative mode ESI. Collision energy not specified. Precursor
m/z 353.2. Retention time ~1.0 min.
COMMENT: NATIVE_RUN_ID 2025.03.26_Julia_Rosangela_NEG_PGF2a.mzML
COMMENT: PROCESSING Conversion to mzML using ProteoWizard
CH$NAME: PGF2a
CH$COMPOUND_CLASS: Lipid; Prostaglandin
CH$FORMULA: C20H34O5
CH$EXACT_MASS: 354.24023
CH$SMILES: CC(=CCC1C(C(CC1CCC(=O)O)O)CCC=C(C)C)O
CH$IUPAC: InChI=1S/C20H34O5/c1-14(2)7-6-8-15-9-10-16(19(22)23)11-12-17(15)13-
18(21)20(24)25/h6,8,15-18H,1,7,9-13H2,2-5H3,(H,22,23)(H,24,25)
CH$LINK: PUBCHEM CID:5280360
CH$LINK: INCHIKEY: PXGPLTODNUVGFL-YNNPMVKQSA-N
AC$INSTRUMENT: Q-Exactive HF, Thermo Scientific
AC$INSTRUMENT_TYPE: LC-ESI-QFT
AC$MASS_SPECTROMETRY: MS_TYPE MS2
AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE
AC$MASS_SPECTROMETRY: IONIZATION ESI
AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE HCD
AC$MASS_SPECTROMETRY: COLLISION_ENERGY unknown
AC$MASS_SPECTROMETRY: RESOLUTION 30.000
MS$FOCUSED_ION: BASE_PEAK 353.2427
MS$FOCUSED_ION: PRECURSOR_M/Z 353.2
MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-
PK$SPLASH: splash10-0002-0900000000-05f3d1d532c7ea5fc3c1
PK$ANNOTATION: m/z annotation exact_mass error(ppm)

235.14 fragment - -
309.21 fragment - -
353.24 precursor 353.2427 0.000
PK$NUM_PEAK: 3
PK$PEAK: m/z int. rel.int.
235.14 5000 13
309.21 8000 22
353.24 36963 100
//

[meier-rene]

Hi Julia,
I'm one of the maintainers of MassBank. It looks to me, that this is your first contribution and your first usage of github as well. I would like to assist you. Maybe we chat a bit here and you tell me what you want to do.
Best, Rene

[JuliaCovic]

Hi Rene,

Thank you very much for reaching out and for your kind offer to help!

To give you some context, I am an undergraduate research student at the Modified Lipids and Redox Biochemistry Laboratory of the Institute of Chemistry at the University of São Paulo (IQ-USP). I am working under the supervision of Prof. Dr. Sayuri Miyamoto, and my research focuses on the construction and dissemination of a high-resolution mass spectrometry library for oxylipins to promote open science.

I am currently trying to deposit the spectra for the PGF2alpha molecule. I have prepared the spectral data according to the project's high-resolution protocols (LC-HRMS), but I am having some difficulties with the submission process.

Since this is my first time using GitHub, I am struggling to understand how the fork process and the GitHub checks/verifications work in relation to MassBank. Specifically, I've encountered some administrative blocks regarding permissions (collaborator status) that are preventing me from completing the fork and opening a Pull Request.

I would really appreciate it if we could chat a bit more so I can better understand these technical steps and successfully contribute our data to MassBank.

Best regards,

Julia Covic Hacker

[meier-rene]

I can help and assist you with all these steps. But before we continue I would like to understand why you are trying to submit your spectrum to MassBank. Normaly we dont take just a single spectrum. Is this just the test to get the data workflow running?

[JuliaCovic]

Hi Rene. Yes, exactly. Submitting the PGF2alpha spectrum is primarily a test to ensure I understand the data workflow and the submission process correctly. Our laboratory has gathered data for several other molecules that have not yet been deposited in the Massbank repository, and once I have successfully navigated the process with this first one, we plan to perform larger deposits in the future.