MassIVE MSV000095290

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GNPS - LBNL_Phage_Nitrogen_Novak_Northen_2024

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Description

The dataset contains LC-MS files for two experiments: 1. 15N-necromass Isotope Labeling Experiment: 20220124_AG_VN_WFNSFVIC_PhageN This experiment examines how phage-lysed (gh-1 phage) and uninfected 15N-labeled and unlabeled Pseudomonas putida necromass affects nitrogen uptake by Brachypodium distachyon and the composition of rhizosphere exometabolites. 2. Necromass Incubation Experiment with and without Plants: 20240229_EB_VN_107432-001_LysTxCtrl This experiment investigates the turnover of bacterial necromass with and without Brachypodium distachyon. For both experiments, filtered P. putida necromass was supplied to plants growing in EcoFAB 2.0 in sterile conditions for one week. The composition of the necromass medium was analyzed at pre-incubation (t0) and post-incubation (t1) using polar (HILIC) metabolite analysis. Each treatment had n=5 biological replicates. Work included in publication: Novak, V., van Winden, M.C.M., Harwood, T.V., Neurath, R., Kosina, S.M., Louie, K.B., Sullivan, M.B., Roux, S., Zengler, K., Mutalik, V.K. and Northen, T.R. (2025), Virocell Necromass Provides Limited Plant Nitrogen and Elicits Rhizosphere Metabolites That Affect Phage Dynamics. Plant, Cell & Environment. https://doi.org/10.1111/pce.15456 [doi:10.25345/C5QZ22V3X] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: exudates ; nitrogen ; plant ; necromass ; isotopes

Contact

Principal Investigators:
(in alphabetical order) 		Trent Northen, Lawrence Berkeley National Laboratory, USA
Vlastimil Novak, Lawrence Berkeley National Laboratory, USA
Submitting User: smkosina
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Experimental Design
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Quantification Results
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GNPS content goes here (MSV000095290 [task=ccbd765f4126477b8049b4704c3aa117])
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

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

"N/A" means no results of this type were submitted.
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.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

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

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.