MassIVE MSV000094570

Partial Public PXD051590

GNPS - Proteomic and metabolomic analysis of multifoliolate mutants of Trifolium repens

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Description

Quadrifoliolate and pentafoliolate mutants of Trifolium repens were collected at Pug Mountain Vineyards in Southern Pennsylvania in the summer of 2023 along with matched trifoliolate plants gathered within the same cubic yard. Stems and leaves were frozen in a dry ice bath and homogenized by beadmill in a solution of methanol, acetonitrile and water (35/35/30). The supernatants were clarified by centrifugation at 13,000 x g for 5 minutes at 4C. The supernatant was removed and dried for metabolomic analysis while the precipitate was dried by speedvac and resuspended in 1x S-Trap lysis buffer. Samples were prepared following vendor instructions using the S-Trap 96-well plate format with the exception that cysteines were not reduced and alkylated. Samples were digested for 2 hours at 47C with a 20 nanograms of trypsin in 100mM TEAB solution. Eluted peptides were dried by SpeedVac and quantified using a colorimetric peptide kit. 400 nanograms of peptides were loaded onto EvoTips and were analyzed using ddaPASEF on a TIMSTOF Flex insturment using a 15cm x 75 um column and the 15SPD and 30SPD methods. Metabolomics was performed on a Q Exactive "Classic" system coupled to an RSLCnano with a 15cm x 2.1mm HyperSil Gold column using a 20min method. Separate runs were performed in triplicate in positive and negative polarities. Proteomic samples were analyzed with FragPipe 21.1 and Metabolomic samples were analyzed in Compound Discoverer 3.3 SP3. [doi:10.25345/C5RN30K14] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Trifolium repens ; 4 leaf clover ; 5 leaf clover ; Proteomics and Metabolomics

Contact

Principal Investigators:
(in alphabetical order) 		Benjamin C Orsburn, Johns Hopkins, USA
Submitting User: ben_orsburn
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GNPS content goes here (MSV000094570 [task=8f5a9d5ddc554da1ad82fc79d712a7a8])
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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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