MassIVE MSV000088323

Imported Reanalysis Dataset Public PXD009712

Pacific Ocean metaproteomics, METZYME KM1128

Description

Global metaproteomic analyses of microbial biomass from the upper water column of the Central Pacific Ocean. This dataset was used as a discovery dataset to identify peptide biomarkers for cyanobacterial populations for use in targeted metaproteomic calibrated multiple reaction monitoring (MRM) analyses published in in Saito et al., 2014 and 2015. Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., and Lamborg, C. H.: Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers, Science, 345, 1173-1177, 2014. Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappé, M. S., DiTullio, G., and Moran, D.: Needles in the Blue Sea: Sub?Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome, PROTEOMICS, 15, 3521-3531, 2015. [doi:10.25345/C5086J] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Metaproteomics proteomics oceanography oceanic proteome

Contact

Principal Investigators:
(in alphabetical order)
Makoto Saito, Marine Chemistry Geochemistry, Woods Hole Oceanographic Institution, US, N/A
Submitting User: ccms

Publications

Saito MA, Bertrand EM, Duffy ME, Gaylord DA, Held NA, Hervey WJ, Hettich RL, Jagtap PD, Janech MG, Kinkade DB, Leary DH, McIlvin MR, Moore EK, Morris RM, Neely BA, Nunn BL, Saunders JK, Shepherd AI, Symmonds NI, Walsh DA.
Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.
J Proteome Res. 2019 Apr 5;18(4):1461-1476. Epub 2019 Mar 12.

Number of Files:
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Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
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Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
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Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
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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.