MassIVE MSV000098188

Partial Public

"Microscale" Salinispora spp. strains (NSSP)

Subscribe Comment Convert Spectra Reanalyze Spectra Add Reanalysis

Description

While our previous evolutionary analyses of Salinispora and its BGCs have focused on 118 strains isolated from worldwide marine sediment samples, the aim of this study was to isolate, genome-sequence, and characterize the biosynthetic potential of a "microscale" collection of Salinispora strains isolated from a 1-m^2 quadrat in Fiji, thus allowing us to compare taxonomic and BGC diversity at different spatial scales. This MassIVE data set contains LCMS runs of the ethyl acetate extracts produced from liquid cultures of 99 microscale Salinispora strains (96 are classified as S. arenicola, 2 as S. pacifica, and 1 as S. oceanensis) grown in A1 media, along with two media controls. The extracts were analyzed on a Agilent 1260 Infinity Series LC system coupled to a 6530 Series Q-TOF mass spectrometer, using a C18 Phenomenex Luna column (5 um, 100 mm x 4.6 mm) with a 10 min solvent gradient from 10% to 100% MeCN (0.1% FA) in water (0.1% FA) with 1.0 mL min-1 flow rate. LCMS parameters: positive mode, source ionization 0 eV, CID 30 eV and a 100-1700 Da detection window. Raw .d and converted .mzxml file formats are included. [doi:10.25345/C5NP1WX11] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Salinispora ; metabolomics ; natural products ; DatasetType:Metabolomics

Contact

Principal Investigators:
(in alphabetical order) 		Paul Jensen, University of California, San Diego, United States
Submitting User: g6castro
Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
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.