MassIVE MSV000082455

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Northern elephant seal outer blubber layer proteome

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Description

Proteins were extracted from the outer (closer to skin) blubber layer of 4 northern elephant seals (Mirounga angustirostris) using either 1) A standard detergent lysis buffer containing 1% sodium deoxycholate, 8 M urea, 5 mM DTT in 50 mM ammonium bicarbonate (SDC method) or 2) the phenol and guanidine thiocyanate reagent Qiazol (QIA method). Mass spectrometry analysis was performed using an Orbitrap Fusion Tribrid mass spectrometer in DDA mode. Briefly, full MS1 scans were resolved by the orbitrap, and ions were selected for MS2 using DDA. These precursor ions were quadrupole filtered and subsequently fragmented using stepped collision HCD. MS2 product ions were resolved by the orbitrap. MS/MS data was analyzed using Proteome Discoverer v2.2. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: blubber ; adipose ; proteome ; marine mammal ; seal ; metabolism

Contact

Principal Investigators:
(in alphabetical order) 		Jane Khudyakov, University of the Pacific, United States
Submitting User: mirounga

Publications

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Khudyakov JI, Deyarmin JS, Hekman RM, Pujade Busqueta L, Maan R, Mody MJ, Banerjee R, Crocker DE, Champagne CD. (2018) A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics. Biology Open doi: 10.1242/bio.036731.

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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.

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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.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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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 protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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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.

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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.

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.