MassIVE MSV000082045

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GNPS_HMP_cultures_full_set

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Description

Extracts of HMP project isolates that were grown successfully. Full dataset. The information on the correspondence of MS data to taxonomy is listed here: https://docs.google.com/spreadsheets/d/1ZaZbwiQS086rDyi_rqzEykz5BFLDMT3YcI0kV7Z9aYA/edit?usp=sharing The document is currently being updated. Sample preparation procedure: The supernatant collected from cell cultures was processed to make it compatible with HLPC-MS analysis. The solid phase extraction with wash was carried out to reduce impact of cell culture media which is highly detrimental for the ESI. The 30 mg sorbent Oasis HLB (Waters, Waltham, MA) SPE cartridges were used to achieve broad metabolite coverage. The cell samples were stored at -80? and thawed at room temperature immediately prior to extraction. The thawed samples were then centrifuged for 10 minutes at 1200 rpm and extracted. For the SPE extraction, the Oasis HLB SPE cartridge was conditioned with 700µL of 100% HPLC grade methanol and equilibrated with 700µL of HPLC grade DI water. The cell supernatant (~350-400µL) was loaded into cartridge and allowed to slowly elute. The loaded SPE wells were then washed with 800µL of 5% methanol in water and the absorbed material was slowly eluted with 200 µL of 100% methanol. Vacuum up to ~ 20 psi was applied for the wells that did not elute within an hour. The collected eluent was stored at -20? until the HPLC-MS analysis. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: bacteria ; cultures ; gut

Contact

Principal Investigators:
(in alphabetical order) 		Pieter Dorrestein, UCSD, United States
Submitting User: aaksenov
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Spectra:
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Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
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GNPS content goes here (MSV000082045 [task=64e3aacbbbfd4b8681e7e788cb6b16fa])
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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.